[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"        "-oTLUAD-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/LUAD-TP/10006018/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/10013790/transformed.cor.cli.txt"

nPatients in clinical file=474, in cluster file=493, common to both=462
[1]  80 462
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              123               339 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              123               339 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              272               190 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              272               190 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              142               320 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              142               320 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              128               334 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              128               334 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               36               426 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               36               426 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               77               385 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               77               385 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               76               386 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               76               386 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               44               418 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               44               418 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              253               209 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              253               209 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              112               350 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              112               350 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              131               331 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              131               331 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               56               406 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               56               406 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              241               221 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              241               221 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              199               263 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              199               263 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              115               347 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              115               347 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              222               240 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              222               240 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               40               422 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               40               422 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               28               434 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               28               434 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               101                361 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               101                361 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                73                389 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                73                389 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                88                374 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                88                374 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               108                354 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               108                354 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               126                336 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               126                336 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               120                342 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               120                342 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                42                420 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                42                420 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               112                350 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               112                350 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                34                428 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                34                428 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               118                344 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               118                344 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                89                373 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                89                373 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                78                384 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                78                384 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               176                286 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               176                286 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                88                374 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                88                374 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                63                399 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                63                399 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                29                433 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                29                433 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                66                396 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                66                396 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               155                307 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               155                307 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               178                284 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               178                284 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                85                377 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                85                377 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                60                402 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                60                402 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               66               396 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               66               396 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               75               387 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               75               387 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               434 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               28               434 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               438 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               438 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               23               439 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               23               439 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              193               269 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              193               269 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              133               329 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              133               329 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              107               355 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              107               355 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              121               341 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              121               341 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               38               424 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               38               424 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              133               329 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              133               329 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               95               367 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               95               367 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              194               268 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              194               268 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               30               432 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               30               432 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               35               427 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               35               427 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              178               284 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              178               284 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               50               412 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               50               412 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              240               222 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              240               222 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              226               236 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              226               236 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               101                361 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               101                361 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               121                341 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               121                341 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               104                358 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               104                358 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                83                379 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                83                379 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                98                364 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                98                364 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                87                375 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                87                375 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               223                239 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               223                239 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               103                359 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               103                359 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               218                244 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               218                244 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               101                361 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               101                361 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               128                334 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               128                334 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               194                268 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               194                268 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                52                410 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                52                410 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               156                306 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               156                306 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               191                271 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               191                271 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               222                240 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               222                240 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               142                320 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               142                320 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               108                354 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               108                354 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                64                398 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                64                398 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               149                313 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               149                313 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               197                265 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               197                265 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               56               406 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               56               406 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "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 462 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-05-4244 TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 
          NA         1523           NA          607          426         1369 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
        1126           NA           NA           NA         1431           NA 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
         578          610           NA           NA          455           NA 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
         761          761          730           NA          457          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         882          670           30           62           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         182          264         2973         3674         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         864         1073          354         1357          448           NA 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1036          190          722         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         723          328          302          845          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         705         1938           NA         1864           NA          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         592          366          218          557           NA          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         535          719          385           99          260          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         466          287          337          351          415           76 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
        2318           NA           NA           NA         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
         445          369          890          522          354           NA 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
          NA         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
        1499          246          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
         653           NA           NA          567          883          764 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
         686           NA           NA           NA           NA           NA 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
          NA         1015           NA          255          105           NA 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
          NA          424          280          701         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
        1375           87            2          993           24           NA 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
        1239           NA           25         1475           NA           NA 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
          NA           67           NA           NA         1826           NA 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1233         2151         1170           18           35          121 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
           6            4           95           40           NA           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
          39           34           24           54           19           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
         197           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
          21          100            6           43           26            4 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8204 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
          47           15           NA           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
         216           44           23           29           11            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
          15          228            9            3          146          202 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         536           15           48           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
          33           42           29           48           NA            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
          28            5           47          162           NA         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
        1289           NA         2696         1445           NA           NA 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
          NA           NA         2067         2199           NA           NA 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        1246          910         1728          628         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1126           NA         2676           62         1305          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        1559          866           31          610          573          427 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         385           NA          174          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         186          690          414          165          230          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
          70           89          382          100           77          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         214           61         1600          711          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         467          131           40          164           38          621 
TCGA-73-7499 TCGA-75-5122 TCGA-75-5125 TCGA-75-5126 TCGA-75-5146 TCGA-75-5147 
         519           NA           NA           NA           NA           NA 
TCGA-75-6203 TCGA-75-6205 TCGA-75-6206 TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 TCGA-78-7143 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
          NA           NA           NA           NA         1093           NA 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1202          760           NA           NA           NA           NA 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1221          678          215           NA         6812           NA 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
          NA           NA           NA           NA           NA          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881           NA          994         6346           NA         2360 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-80-5611 TCGA-83-5908 
          NA           NA           NA           NA           NA          824 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
          NA           NA           11          630          422           NA 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
         591           NA          508          745           10           NA 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
          13           24          479          489          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
          16           NA           19           26           35           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          34           18           15          455          405           10 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
          30           NA           14           39          323           NA 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
          60          310           79          417          372          842 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         224           35          492          197          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 
          44          218          297          127          186           34 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
           2          568          377          477          476          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         964         1965         1932         1332          775          181 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
          NA           22          107          182           NA           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
         147           15          148          115          197          271 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         392          427          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         116            6          285          622          353           NA 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
          NA          142           NA           NA           NA         1490 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=118,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=279,	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=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=90,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=22,	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 462 columns, 1 survival variables, and 13 non-survival variables.
AGE, nv=50, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=8, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
143 259  40  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
143 259  40  18 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
143 259  40  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
143 259  40  18 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
295  85  70   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  295    85    72 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
295  85  70   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  295    85    72 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=12, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=90, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    82  27
  1P GAIN WILD-TYPE 239  55
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              109               294 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               27                55 
$`1P GAIN MUTATED`
TCGA-05-4382 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-5423 
         607          912          913          791          761          151 
TCGA-05-5428 TCGA-05-5429 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2659 
         670           30         1357          448         1429         1367 
TCGA-44-2662 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 
        1280          705         1864         1978          218         1970 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47B TCGA-44-A4SU TCGA-49-4501 
         719          385           99          287           76         1421 
TCGA-49-4505 TCGA-49-4510 TCGA-49-6742 TCGA-49-6744 TCGA-50-5045 TCGA-50-5068 
         428          896          445          890         2174         1499 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
         246          267         2370          567          764          686 
TCGA-50-6597 TCGA-55-1592 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 
        1015          701           24         1239           67         1826 
TCGA-55-7281 TCGA-55-7573 TCGA-55-7576 TCGA-55-7911 TCGA-55-8089 TCGA-55-8096 
          18            4           40           21          100           47 
TCGA-55-8206 TCGA-55-8514 TCGA-55-A48X TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          46          202           33            5           47          162 
TCGA-62-8399 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5781 TCGA-67-6217 
        2696         1728         1686         1968         1559          422 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
         382          100           77          129          214           61 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 
         467          131          164         1967         1965         1973 
TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 
        1950         1948         1957          215         1940         1937 
TCGA-78-7535 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-86-7953 TCGA-86-8055 
        1972         1952         1949         1981          591           10 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 TCGA-86-8673 
          24          479          482           16           35          455 
TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 
          10           14          323          310          372          842 
TCGA-95-7039 TCGA-95-7944 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8177 
          34          377          964         1332          181          147 
TCGA-97-8552 TCGA-99-7458 TCGA-J2-A4AG TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4TC 
         115          392          238          285         1967         1944 
TCGA-MP-A4TF 
        1970 

$`1P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
        1523          426         1369         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
         578          610         1958         1997          455          365 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 
         669          791          761          730          457          882 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
        1971          133         1324          400          741         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
         722         1013          863          383          723          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 
         302          845          704          658         1938         1942 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 
         444          592          366          557          882          535 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         260          486          466          337          351          415 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
        1932         1081          999          268          157         1700 
TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         369          522          354         2146          455          785 
TCGA-50-5066 TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 TCGA-50-7109 
         944          282         1091          653          883          255 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
         105         1986         1971          424          280         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6971 
        1479         1375           87            2          993           25 
TCGA-55-6972 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 
        1475         1233         2151         1170           35          121 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
           6           95         1958           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 
          24           54           19           16          197            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
          31            5           33           21            6           43 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 
          26            4           15           33           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          44           23           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 
         228            9            3          146          536           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
          48           49           66          106           42           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-62-8395 TCGA-62-8397 
          48         1952            1           28         1216         1289 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1970         1445         2067         2199         1246          910 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
         628         1189         1126         1959           62         1305 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
         864          866           31          610          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         385          174          141          202          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         414          165          230          184           70           89 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4675 TCGA-73-4677 
        1600          711          912          800           40           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 
         621          519         1970         1956         1988         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
        1093         1963         1202          760         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 
        1221          678         1950         1934         1965         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 
        1944          327          881          994         1971         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1964         1965         1972          824         1959           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         630          422         1968         1963          508          745 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8358 
        1963           13          489          476         1955           19 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
          26           45           34           18           15          405 
TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
          30           39         1940           60           79          417 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         224           35          492          197          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 
          44          218          297          127          186            2 
TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 
         568          477          476          121         1965         1932 
TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
         775           22          107          182         1965           87 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 
          15          148          197          271          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
          44          170          154          114          287          282 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 
         578          435          116            6          622          353 
TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1946         1951         1954         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1970          142         1955         1971         1490 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                 1 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             2696              2199 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            467.0             462.5 
[1] "4.0 - 2696.0 (467.0)" "1.0 - 2199.0 (462.5)"
[1] "hr=" "1"  
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  1P GAIN MUTATED         2       28       35        14        21         14
  1P GAIN WILD-TYPE       2       85       96        29        48         53
                   vv
clus                STAGE IIIB STAGE IV
  1P GAIN MUTATED            2        6
  1P GAIN WILD-TYPE          9       17
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                28                85
  STAGE IB                35                96
  STAGE IIA               14                29
  STAGE IIB               21                48
  STAGE IIIA              14                53
  STAGE IIIB               2                 9
  STAGE IV                 6                17
[1] 8 2
[1] 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    40  71   8   4
  1P GAIN WILD-TYPE 103 188  32  14
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              40               103
  T2              71               188
  T3               8                32
  T4               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                 N0  N1 N2+N3
  1P GAIN MUTATED    75  32    14
  1P GAIN WILD-TYPE 220  53    58
D1V5, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0                 75               220
  N1                 32                53
  N2+N3              14                58
[1] 3 2
[1] 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 M1B  MX
  1P GAIN MUTATED    88   6   0   0  27
  1P GAIN WILD-TYPE 229  12   1   3  92
D1V6, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               88               229
  M1                6                12
  M1A               0                 1
  M1B               0                 3
  MX               27                92
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    68  55
  1P GAIN WILD-TYPE 180 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     68   55
  1P GAIN WILD-TYPE  180  159
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              68               180
  MALE                55               159
[1] 2 2
[1] FALSE
D1V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1P GAIN MUTATED                            2
  1P GAIN WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1P GAIN MUTATED                                  20
  1P GAIN WILD-TYPE                                73
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                   84
  1P GAIN WILD-TYPE                                                210
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1P GAIN MUTATED                                            0
  1P GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  1P GAIN MUTATED                                               7
  1P GAIN WILD-TYPE                                            12
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  1P GAIN MUTATED                                0
  1P GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  1P GAIN MUTATED                                    2
  1P GAIN WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  1P GAIN MUTATED                              0                             4
  1P GAIN WILD-TYPE                            2                            15
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  1P GAIN MUTATED                                 0
  1P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  1P GAIN MUTATED                                               2
  1P GAIN WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  1P GAIN MUTATED                              2
  1P GAIN WILD-TYPE                            5
D1V9, multiclass
                                                    clus
vv                                                   1P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              84
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    7
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   1P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               210
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     12
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     15
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  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     4 119
  1P GAIN WILD-TYPE  17 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4  119
  1P GAIN WILD-TYPE   17  322
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                4                17
  YES             119               322
[1] 2 2
[1] FALSE
D1V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    80   4   1   3
  1P GAIN WILD-TYPE 238   7   3  16
D1V12, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              80               238
  R1               4                 7
  R2               1                 3
  RX               3                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  1     2
  1P GAIN WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          10    94
  1P GAIN WILD-TYPE                        16   268
D1V13, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                     10                16
  WHITE                                         94               268
[1] 4 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     2  82
  1P GAIN WILD-TYPE   5 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   82
  1P GAIN WILD-TYPE    5  250
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              82               250
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   193  48
  1Q GAIN WILD-TYPE 128  34
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              241               162 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               48                34 
$`1Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4410 
        1523          607          426         1369         1126         1958 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 
        1997          455          912          913          761          761 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         457          151          882          670           30           62 
TCGA-35-3615 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 TCGA-38-4632 TCGA-38-6178 
          14         1952         1492          864         1357          448 
TCGA-38-7271 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-2668 TCGA-44-5645 
        1971         1429         1367         1280          246          383 
TCGA-44-6144 TCGA-44-6147 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         723          845          705         1938         1942         1864 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
        1978          444          218         1970          882          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
         719          385           99          466          287          337 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         415           76         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4510 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-50-5045 
         999          896          445          369          890         2174 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
         455         1499          246          267         2370          653 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-8460 TCGA-53-7626 
         567          764          686         1015          105         1971 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
         424          701         1375          993           24         1239 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1475           67         1826         1170           18           35 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 
         121            4           95           40           39           34 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          54           19           16          197           21            3 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
           5           33           21          100           26            4 
TCGA-55-8096 TCGA-55-8206 TCGA-55-8301 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
          47           46           44           11           15          228 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-A48X 
           9          202           15           48           49           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF 
          42           29         1952            1            5           47 
TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 
         162         1970         2696         1728         1686         1126 
TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 
        1968          864         1559          610          573          385 
TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
         174          422          202          186          414          165 
TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
         230           89          382          100           77          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 
         214           61         1600          711          912          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-7025 
         131           40          164           38          621         1967 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1965         1973         1950         1944         1093         1963 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
         760         1948         1961         1963         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
         215         1940         1937         1972         1944          327 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 TCGA-80-5608 TCGA-86-7701 TCGA-86-7713 
         994         1949         1981         1972           11          422 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 
         591         1963          745           10           24          479 
TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 
         489          482           16         1955           26           35 
TCGA-86-8669 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          34          455          405           10           30           14 
TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
         323          310           79          372          842           35 
TCGA-91-7771 TCGA-91-8496 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 
         492          197          127          186           34          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 
         377          477          121          964         1965         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
         775          181          182          147           15          115 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD 
         271          392           44          170          114          287 
TCGA-J2-A4AG TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         238          116            6          285          622          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH 
        1946         1967         1954         1944         1970          142 
TCGA-MP-A5C7 
        1490 

$`1Q GAIN WILD-TYPE`
TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4422 TCGA-05-4425 
        1947         1431          578          610          365          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         791          791          730          225          182          264 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 TCGA-38-A44F TCGA-44-2655 
        1962         1147         1073          354          133         1324 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
         400          741         1301           97         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6145 
        1036          190          722         1013          863          328 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 
         302          704          658          592          366          557 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
         260          486          351          268          157         1700 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 
         522          354         2146          785          944          282 
TCGA-50-5932 TCGA-50-5942 TCGA-50-7109 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1594 
        1091          883          255         1986          280         1178 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6971 TCGA-55-6985 TCGA-55-6986 
        1479           87            2           25         1233         2151 
TCGA-55-7570 TCGA-55-7724 TCGA-55-7726 TCGA-55-7728 TCGA-55-7994 TCGA-55-8090 
           6         1958           39           24           31            6 
TCGA-55-8091 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 TCGA-55-8302 
          43           15           33           66          216           23 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8620 
          29            8            3          146          536           66 
TCGA-55-8621 TCGA-55-A490 TCGA-55-A493 TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 
         106           48           28         1216         1289         1445 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
        2067         2199         1246          910          628         1189 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 
        1959           62         1305          866           31          427 
TCGA-67-6216 TCGA-69-7763 TCGA-69-7974 TCGA-69-7978 TCGA-73-4666 TCGA-73-7499 
         141          690          184           70          800          519 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7152 TCGA-78-7155 TCGA-78-7163 
        1970         1956         1988         1202         1957         1950 
TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
        1934         1965         1949          881         1952         1971 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 
        1954         1964         1965          824         1959          630 
TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8278 TCGA-86-8358 
        1968          508         1963           13          476           19 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
          45           18           15           39         1940           60 
TCGA-91-6836 TCGA-91-6848 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         417          224          174           36           44          218 
TCGA-93-7347 TCGA-95-7043 TCGA-95-7948 TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 
         297            2          476         1932           22          107 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M2 TCGA-99-8025 TCGA-99-8028 
        1965           87          148          197          427          459 
TCGA-J2-8192 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MP-A4T2 TCGA-MP-A4T4 
         154          282          578          435         1951         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1957         1980         1951         1970         1955         1971 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                 2 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             2696              2199 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            428.0             567.5 
[1] "1.0 - 2696.0 (428.0)" "2.0 - 2199.0 (567.5)"
[1] "hr=" "1.2"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  1Q GAIN MUTATED         2       71       77        26        40         33
  1Q GAIN WILD-TYPE       2       42       54        17        29         34
                   vv
clus                STAGE IIIB STAGE IV
  1Q GAIN MUTATED            8       14
  1Q GAIN WILD-TYPE          3        9
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                71                42
  STAGE IB                77                54
  STAGE IIA               26                17
  STAGE IIB               40                29
  STAGE IIIA              33                34
  STAGE IIIB               8                 3
  STAGE IV                14                 9
[1] 8 2
[1] 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    87 147  25  12
  1Q GAIN WILD-TYPE  56 112  15   6
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              87                56
  T2             147               112
  T3              25                15
  T4              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                 N0  N1 N2+N3
  1Q GAIN MUTATED   175  51    37
  1Q GAIN WILD-TYPE 120  34    35
D2V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                175               120
  N1                 51                34
  N2+N3              37                35
[1] 3 2
[1] 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 M1B  MX
  1Q GAIN MUTATED   185  12   0   1  71
  1Q GAIN WILD-TYPE 132   6   1   2  48
D2V6, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              185               132
  M1               12                 6
  M1A               0                 1
  M1B               1                 2
  MX               71                48
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   140 132
  1Q GAIN WILD-TYPE 108  82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    140  132
  1Q GAIN WILD-TYPE  108   82
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE             140               108
  MALE               132                82
[1] 2 2
[1] FALSE
D2V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1Q GAIN MUTATED                           10
  1Q GAIN WILD-TYPE                          3
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1Q GAIN MUTATED                                  53
  1Q GAIN WILD-TYPE                                40
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                  172
  1Q GAIN WILD-TYPE                                                122
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1Q GAIN MUTATED                                            0
  1Q GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  1Q GAIN MUTATED                                              14
  1Q GAIN WILD-TYPE                                             5
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  1Q GAIN MUTATED                                1
  1Q GAIN WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  1Q GAIN MUTATED                                    2
  1Q GAIN WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  1Q GAIN MUTATED                              0                            13
  1Q GAIN WILD-TYPE                            2                             6
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  1Q GAIN MUTATED                                 0
  1Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  1Q GAIN MUTATED                                               3
  1Q GAIN WILD-TYPE                                             1
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  1Q GAIN MUTATED                              4
  1Q GAIN WILD-TYPE                            3
D2V9, multiclass
                                                    clus
vv                                                   1Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                      10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             172
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   14
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                   13
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     4
                                                    clus
vv                                                   1Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               122
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      5
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                      6
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      1
  MUCINOUS (COLLOID) CARCINOMA                                       3
[1] 12  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    10 262
  1Q GAIN WILD-TYPE  11 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     10  262
  1Q GAIN WILD-TYPE   11  179
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               10                11
  YES             262               179
[1] 2 2
[1] FALSE
D2V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED   183   8   2  13
  1Q GAIN WILD-TYPE 135   3   2   6
D2V12, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             183               135
  R1               8                 3
  R2               2                 2
  RX              13                 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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1     4
  1Q GAIN WILD-TYPE                                0     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          17   215
  1Q GAIN WILD-TYPE                         9   147
D2V13, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 2
  BLACK OR AFRICAN AMERICAN                     17                 9
  WHITE                                        215               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"
D2V14, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     3 196
  1Q GAIN WILD-TYPE   4 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3  196
  1Q GAIN WILD-TYPE    4  136
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             196               136
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED   104  19
  2P GAIN WILD-TYPE 217  63
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              123               280 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               19                63 
$`2P GAIN MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         607         1369         1126         1997          455          912 
TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 
         913          761          882          670          225          182 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2657 TCGA-44-3918 
        1073          354         1357          448          400         1036 
TCGA-44-6779 TCGA-44-7667 TCGA-44-7670 TCGA-44-A47A TCGA-44-A47G TCGA-49-4507 
        1978          557          882          466          351          268 
TCGA-49-4510 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-50-5072 TCGA-50-5946 
         896          445          369          890          246          686 
TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
        1015         1986          424          280          701         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 
        1479         1375         1826           18           35            4 
TCGA-55-7576 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8096 
          40           16          197           21            5           47 
TCGA-55-8205 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8615 TCGA-55-8616 
          33            8          228            9           15           48 
TCGA-55-8620 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8402 TCGA-64-1678 
          66           28            5          162         1445         1189 
TCGA-64-1680 TCGA-64-5774 TCGA-67-3770 TCGA-67-6217 TCGA-69-7764 TCGA-69-7973 
        1126         1959           31          422          414          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 TCGA-73-4662 TCGA-73-4668 
         184           70          382          129          912          467 
TCGA-73-4675 TCGA-73-4676 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
          40          164         1970         1967         1956         1965 
TCGA-78-7145 TCGA-78-7149 TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1973         1093         1957         1221          678          215 
TCGA-78-7163 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 
        1950          327          994         1949         1981         1964 
TCGA-80-5608 TCGA-86-7711 TCGA-86-7713 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
        1972          630          422          508          745           10 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 TCGA-91-6829 TCGA-91-6831 
          26           35           34          455         1940          310 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-95-7043 TCGA-95-7567 
          79          417          372          842            2          568 
TCGA-95-7944 TCGA-95-A4VK TCGA-97-7547 TCGA-97-8179 TCGA-99-8025 TCGA-99-8032 
         377          121         1965           15          427           44 
TCGA-99-8033 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
         170          114          116            6          285          353 
TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TK 
        1980         1944         1971 

$`2P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        1523          426         1947         1431          578          610 
TCGA-05-4410 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
        1958          365          669          791          791          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         730          457          151           30           62           14 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
         264         1952         1962         1147         1492          864 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 
        1971          133         1324         1429         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
         190          722         1013          863          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
        1938         1942         1864          444          592          366 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
         218         1970          535          719          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU 
         260          486          287          337          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 
        1932         1081         1421          428          999          157 
TCGA-49-4514 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
        1700          522          354         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         785          944         1499          282          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 
        2370          653          567          883          764          255 
TCGA-50-8460 TCGA-53-7626 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
         105         1971           87            2          993           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 
        1239           25         1475           67         1233         2151 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
        1170          121            6           95         1958           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7914 
          39           34           24           54           19            3 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
          31           33           21          100            6           43 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
          26            4           15           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 
          44           23           29           11           15            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
         146          202          536           49          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
          42           29           48         1952            1           47 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V 
        1216         1289         1970         2696         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
        1246          910         1728          628         1686         1968 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
          62         1305          864         1559          866          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
         573          427          385          174          141          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
         186          690          165           89          100           77 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 
         214           61         1600          711          800          131 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
          38          621          519         1988         1950         1944 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
        1963         1202          760         1948         1961         1963 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1940         1934         1937         1965         1972         1949 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 
        1944          881         1952         1971         1954         1965 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
         824         1959           11         1968          591         1963 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        1963           13           24          479          489          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 
         482           16         1955           19           45           18 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
          15          405           10           30           14           39 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         323           60          224           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         174           36           44          218          297          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-7552 
         186           34          477          476          964         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1332          775          181           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
        1965           87          147          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE 
         271          392          459          154          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
         238          578          435          622         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE 
        1951         1954         1954         1957         1951         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1970          142         1955         1490 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                 1 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1997              2696 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              427               484 
[1] "2.0 - 1997.0 (427.0)" "1.0 - 2696.0 (484.0)"
[1] "hr=" "1.4"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  2P GAIN MUTATED         1       36       37        16        17         23
  2P GAIN WILD-TYPE       3       77       94        27        52         44
                   vv
clus                STAGE IIIB STAGE IV
  2P GAIN MUTATED            4        8
  2P GAIN WILD-TYPE          7       15
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                36                77
  STAGE IB                37                94
  STAGE IIA               16                27
  STAGE IIB               17                52
  STAGE IIIA              23                44
  STAGE IIIB               4                 7
  STAGE IV                 8                15
[1] 8 2
[1] 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    42  78  14   6
  2P GAIN WILD-TYPE 101 181  26  12
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              42               101
  T2              78               181
  T3              14                26
  T4               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                 N0  N1 N2+N3
  2P GAIN MUTATED    84  30    25
  2P GAIN WILD-TYPE 211  55    47
D3V5, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0                 84               211
  N1                 30                55
  N2+N3              25                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  2P GAIN MUTATED    99   7   0   1  34
  2P GAIN WILD-TYPE 218  11   1   2  85
D3V6, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               99               218
  M1                7                11
  M1A               0                 1
  M1B               1                 2
  MX               34                85
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    79  63
  2P GAIN WILD-TYPE 169 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     79   63
  2P GAIN WILD-TYPE  169  151
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              79               169
  MALE                63               151
[1] 2 2
[1] FALSE
D3V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2P GAIN MUTATED                            3
  2P GAIN WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2P GAIN MUTATED                                  33
  2P GAIN WILD-TYPE                                60
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                   90
  2P GAIN WILD-TYPE                                                204
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2P GAIN MUTATED                                            0
  2P GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  2P GAIN MUTATED                                               5
  2P GAIN WILD-TYPE                                            14
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  2P GAIN MUTATED                                2
  2P GAIN WILD-TYPE                              0
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  2P GAIN MUTATED                                    1
  2P GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  2P GAIN MUTATED                              0                             4
  2P GAIN WILD-TYPE                            2                            15
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  2P GAIN MUTATED                                 0
  2P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  2P GAIN MUTATED                                               2
  2P GAIN WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  2P GAIN MUTATED                              2
  2P GAIN WILD-TYPE                            5
D3V9, multiclass
                                                    clus
vv                                                   2P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              90
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    5
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   2P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               204
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     14
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     15
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  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     5 137
  2P GAIN WILD-TYPE  16 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5  137
  2P GAIN WILD-TYPE   16  304
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                5                16
  YES             137               304
[1] 2 2
[1] FALSE
D3V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED   101   6   2   6
  2P GAIN WILD-TYPE 217   5   2  13
D3V12, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0             101               217
  R1               6                 5
  R2               2                 2
  RX               6                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  1     2
  2P GAIN WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           6   107
  2P GAIN WILD-TYPE                        20   255
D3V13, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      6                20
  WHITE                                        107               255
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     5  95
  2P GAIN WILD-TYPE   2 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5   95
  2P GAIN WILD-TYPE    2  237
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO              95               237
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    93  19
  2Q GAIN WILD-TYPE 228  63
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              112               291 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19                63 
$`2Q GAIN MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 
         607         1369         1126          610         1958         1997 
TCGA-05-4417 TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 
         455          913          761          882          670          225 
TCGA-35-5375 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-44-2657 TCGA-44-3918 
         264         1073         1357          448          400         1036 
TCGA-44-7662 TCGA-44-7670 TCGA-44-A47A TCGA-44-A47G TCGA-49-4505 TCGA-49-4507 
         218          882          466          351          428          268 
TCGA-49-4510 TCGA-49-6742 TCGA-49-6744 TCGA-50-5072 TCGA-50-6597 TCGA-53-7624 
         896          445          890          246         1015         1986 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6983 
         424          280          701         1178         1375         1826 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7726 TCGA-55-7907 
          18           35            4           40           39           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8096 TCGA-55-8205 TCGA-55-8207 
         197           21            5           47           33           66 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 TCGA-55-8620 TCGA-55-A493 
           8          228          202           15           66           28 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8402 TCGA-62-A471 TCGA-64-1680 TCGA-67-3770 
           5          162         1445         1246         1126           31 
TCGA-67-3771 TCGA-67-6217 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         610          422          414          230          184           70 
TCGA-69-7980 TCGA-69-8255 TCGA-73-4662 TCGA-73-4675 TCGA-75-6214 TCGA-75-7025 
         382          129          912           40         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7149 TCGA-78-7155 TCGA-78-7160 TCGA-78-7162 
        1956         1965         1093         1957          678         1940 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 
        1950         1937         1965          327          994         1949 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 TCGA-86-7713 TCGA-86-8055 
        1981         1964         1972         1959          422           10 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 TCGA-91-6829 TCGA-91-6835 
          26           35           34          455         1940           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
         417          372          842            2          568          377 
TCGA-97-7547 TCGA-97-8179 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8194 TCGA-L9-A444 
        1965           15          427          170          114            6 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T9 TCGA-MP-A4TC 
         285          353         1980         1944 

$`2Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4420 
        1523          426         1947         1431          578          912 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
         365          669          791          791          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 
         457          151           30           62           14          182 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 
        1952         1962         1147         1492          864          354 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 
        1971          133         1324         1429         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
         190          722         1013          863          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
        1938         1942         1864         1978          444          592 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         366          557         1970          535          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS 
          99          260          486          287          337          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4512 
          76         1932         1081         1421          999          157 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
        1700          369          522          354         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
         455          785          944         1499          282          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-55-1595 TCGA-55-5899 
         686          255          105         1971         1479           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
           2          993           24         1239           25         1475 
TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 
          67         1233         2151         1170          121            6 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
          95         1958           39           34           24           54 
TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
          19            3           31           33           21          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 
           6           43           26            4           15           46 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
         216           44           23           29           11           15 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
           9            3          146          536           48           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
         106           33           42           29           48         1952 
TCGA-55-A492 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
           1           47         1216         1289         1970         2696 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
        2067         2199          910         1728          628         1189 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1686         1968         1959           62         1305          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
        1559          866          573          427          385          174 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7979 
         141          202          186          690          165           89 
TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         100           77          214           61         1600          711 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         800          467          131          164           38          621 
TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
         519         1973         1988         1950         1944         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1202          760         1948         1961         1963         1221 
TCGA-78-7161 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
         215         1934         1972         1949         1944          881 
TCGA-78-7542 TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 TCGA-83-5908 TCGA-86-7701 
        1952         1971         1954         1965          824           11 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         630         1968          591         1963          508          745 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        1963           13           24          479          489          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 
         482           16         1955           19           45           18 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
          15          405           10           30           14           39 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
         323           60          310          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
         127          186           34          477          476          121 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
         964         1932         1332          775          181           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 
         107          182         1965           87          147          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
         115          197          271          392          459           44 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         154          287          282          238          578          435 
TCGA-L9-A443 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         116          622         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1954         1957         1951         1970         1970          142 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                 1 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1997              2696 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            427.5             482.0 
[1] "2.0 - 1997.0 (427.5)" "1.0 - 2696.0 (482.0)"
[1] "hr=" "1.2"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  2Q GAIN MUTATED         1       32       34        14        14         22
  2Q GAIN WILD-TYPE       3       81       97        29        55         45
                   vv
clus                STAGE IIIB STAGE IV
  2Q GAIN MUTATED            4        7
  2Q GAIN WILD-TYPE          7       16
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                32                81
  STAGE IB                34                97
  STAGE IIA               14                29
  STAGE IIB               14                55
  STAGE IIIA              22                45
  STAGE IIIB               4                 7
  STAGE IV                 7                16
[1] 8 2
[1] 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    37  72  12   5
  2Q GAIN WILD-TYPE 106 187  28  13
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              37               106
  T2              72               187
  T3              12                28
  T4               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                 N0  N1 N2+N3
  2Q GAIN MUTATED    76  27    23
  2Q GAIN WILD-TYPE 219  58    49
D4V5, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0                 76               219
  N1                 27                58
  N2+N3              23                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  2Q GAIN MUTATED    90   6   0   1  30
  2Q GAIN WILD-TYPE 227  12   1   2  89
D4V6, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               90               227
  M1                6                12
  M1A               0                 1
  M1B               1                 2
  MX               30                89
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    67  61
  2Q GAIN WILD-TYPE 181 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     67   61
  2Q GAIN WILD-TYPE  181  153
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              67               181
  MALE                61               153
[1] 2 2
[1] FALSE
D4V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2Q GAIN MUTATED                            3
  2Q GAIN WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2Q GAIN MUTATED                                  34
  2Q GAIN WILD-TYPE                                59
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                   77
  2Q GAIN WILD-TYPE                                                217
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2Q GAIN MUTATED                                            0
  2Q GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  2Q GAIN MUTATED                                               5
  2Q GAIN WILD-TYPE                                            14
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  2Q GAIN MUTATED                                0
  2Q GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  2Q GAIN MUTATED                                    0
  2Q GAIN WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  2Q GAIN MUTATED                              0                             5
  2Q GAIN WILD-TYPE                            2                            14
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  2Q GAIN MUTATED                                 0
  2Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  2Q GAIN MUTATED                                               2
  2Q GAIN WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  2Q GAIN MUTATED                              2
  2Q GAIN WILD-TYPE                            5
D4V9, multiclass
                                                    clus
vv                                                   2Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              77
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    5
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    5
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   2Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               217
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     14
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     14
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  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     5 123
  2Q GAIN WILD-TYPE  16 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5  123
  2Q GAIN WILD-TYPE   16  318
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                5                16
  YES             123               318
[1] 2 2
[1] FALSE
D4V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    94   4   2   4
  2Q GAIN WILD-TYPE 224   7   2  15
D4V12, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              94               224
  R1               4                 7
  R2               2                 2
  RX               4                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     1
  2Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           8    94
  2Q GAIN WILD-TYPE                        18   268
D4V13, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      8                18
  WHITE                                         94               268
[1] 4 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     4  86
  2Q GAIN WILD-TYPE   3 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   86
  2Q GAIN WILD-TYPE    3  246
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO              86               246
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    26   5
  3P GAIN WILD-TYPE 295  77
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               31               372 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                77 
$`3P GAIN MUTATED`
TCGA-05-4410 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-5428 TCGA-35-5375 
        1958          912          913          791          670          264 
TCGA-44-A47B TCGA-49-4507 TCGA-49-6743 TCGA-50-5946 TCGA-53-A4EZ TCGA-55-6972 
         287          268          369          686          280         1475 
TCGA-55-7903 TCGA-55-7995 TCGA-64-1677 TCGA-64-5775 TCGA-69-7760 TCGA-69-7974 
          19            5          628           62          202          184 
TCGA-69-7978 TCGA-69-A59K TCGA-73-4676 TCGA-78-7145 TCGA-78-8662 TCGA-86-7711 
          70          214          164         1973         1964          630 
TCGA-86-7953 TCGA-86-8074 TCGA-86-8075 TCGA-91-6828 TCGA-J2-A4AD TCGA-L9-A443 
         591           24          479          323          287          116 
TCGA-L9-A444 
           6 

$`3P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
        1431          578          610         1997          455          365 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         669          791          761          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         151          882           30           62           14          225 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
         182         1952         1962         1147         1492          864 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
        1073          354         1357          448         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
        1324         1429          400         1367          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
         190          722         1013          863          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
        1938         1942         1864         1978          444          592 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         366          218          557         1970          882          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
         719          385           99          260          486          466 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         337          351          415           76         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
        1421          428          999          896          157         1700 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
         445          890          522          354         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         267         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         764         1015          255          105         1986         1971 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         424          701         1178         1479         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 
           2          993           24         1239           25           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1826         1233         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
          39           39           34           24           54           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
         197           21            3           31           33           21 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
         100            6           43           26            4           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
          15           33           46           66          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
          23           29           11            8           15          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
           9            3          146          202          536           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
          48           49           66          106           33           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          29           48         1952            1           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
          47          162         1216         1289         1970         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
        1445         2067         2199         1246          910         1728 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
        1189         1686         1126         1968         1959         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
         864         1559          866           31          610          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 
         427          385          174          141          422          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 
         690          414          165          230           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         100           77          129           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
         912          800          467          131           40           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         621          519         1970         1967         1956         1965 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1988         1950         1944         1093         1963         1202 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
         760         1948         1957         1961         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          215         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1965         1972         1949         1944          327          881 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
        1952          994         1949         1971         1981         1954 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 
        1965         1972          824         1959           11          422 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
        1968         1963          508          745           10         1963 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
          13          489          476          482           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          19           26           35           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          15          455          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          39         1940           60          310           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         372          842          224           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         174           36           44          218          297          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         186           34            2          568          377          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         476          121          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
         775          181           22          107          182         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
          87          147           15          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         271          392          427          459           44          170 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         154          114          282          238          578          435 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         285          622          353         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1954         1954         1957         1980         1951         1944 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1970          142         1955         1971         1490 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                 1 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1973              2696 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              287               476 
[1] "5.0 - 1973.0 (287.0)" "1.0 - 2696.0 (476.0)"
[1] "hr=" "1.3"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  3P GAIN MUTATED         0       10        7         5         6          6
  3P GAIN WILD-TYPE       4      103      124        38        63         61
                   vv
clus                STAGE IIIB STAGE IV
  3P GAIN MUTATED            0        2
  3P GAIN WILD-TYPE         11       21
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                10               103
  STAGE IB                 7               124
  STAGE IIA                5                38
  STAGE IIB                6                63
  STAGE IIIA               6                61
  STAGE IIIB               0                11
  STAGE IV                 2                21
[1] 8 2
[1] 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    13  16   4   3
  3P GAIN WILD-TYPE 130 243  36  15
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              13               130
  T2              16               243
  T3               4                36
  T4               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                 N0  N1 N2+N3
  3P GAIN MUTATED    21  11     4
  3P GAIN WILD-TYPE 274  74    68
D5V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                 21               274
  N1                 11                74
  N2+N3               4                68
[1] 3 2
[1] 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 M1B  MX
  3P GAIN MUTATED    24   2   0   0  10
  3P GAIN WILD-TYPE 293  16   1   3 109
D5V6, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               24               293
  M1                2                16
  M1A               0                 1
  M1B               0                 3
  MX               10               109
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    19  17
  3P GAIN WILD-TYPE 229 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     19   17
  3P GAIN WILD-TYPE  229  197
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              19               229
  MALE                17               197
[1] 2 2
[1] FALSE
D5V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3P GAIN MUTATED                            2
  3P GAIN WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3P GAIN MUTATED                                  10
  3P GAIN WILD-TYPE                                83
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                   21
  3P GAIN WILD-TYPE                                                273
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3P GAIN MUTATED                                            0
  3P GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  3P GAIN MUTATED                                               1
  3P GAIN WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  3P GAIN MUTATED                                1
  3P GAIN WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  3P GAIN MUTATED                                    0
  3P GAIN WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  3P GAIN MUTATED                              0                             1
  3P GAIN WILD-TYPE                            2                            18
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  3P GAIN MUTATED                                 0
  3P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  3P GAIN MUTATED                                               0
  3P GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  3P GAIN MUTATED                              0
  3P GAIN WILD-TYPE                            7
D5V9, multiclass
                                                    clus
vv                                                   3P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              21
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   3P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               273
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     18
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  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     3  33
  3P GAIN WILD-TYPE  18 408
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   33
  3P GAIN WILD-TYPE   18  408
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                3                18
  YES              33               408
[1] 2 2
[1] FALSE
D5V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    23   2   1   4
  3P GAIN WILD-TYPE 295   9   3  15
D5V12, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              23               295
  R1               2                 9
  R2               1                 3
  RX               4                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     0
  3P GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           1    27
  3P GAIN WILD-TYPE                        25   335
D5V13, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                25
  WHITE                                         27               335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  22
  3P GAIN WILD-TYPE   5 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   22
  3P GAIN WILD-TYPE    5  310
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              22               310
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    57  11
  3Q GAIN WILD-TYPE 264  71
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               68               335 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               11                71 
$`3Q GAIN MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4410 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 
         607         1369         1958          912          913          791 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-5375 TCGA-38-4626 TCGA-44-2662 
         882          670           30          264         1962         1280 
TCGA-44-2668 TCGA-44-3918 TCGA-44-5643 TCGA-44-6145 TCGA-44-6147 TCGA-44-7660 
         246         1036         1013          328          845          592 
TCGA-44-7670 TCGA-44-A47B TCGA-49-4507 TCGA-49-6743 TCGA-50-5072 TCGA-50-5931 
         882          287          268          369          246          267 
TCGA-50-5941 TCGA-50-5946 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6972 TCGA-55-7724 
         567          686          280         1178         1475         1958 
TCGA-55-7726 TCGA-55-7903 TCGA-55-7995 TCGA-55-8085 TCGA-55-8205 TCGA-55-8614 
          39           19            5           33           33          536 
TCGA-55-A490 TCGA-55-A491 TCGA-64-1679 TCGA-64-5815 TCGA-69-7760 TCGA-69-7978 
          48         1952         1686          866          202           70 
TCGA-69-7980 TCGA-69-A59K TCGA-73-4676 TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 
         382          214          164          519         1973         1988 
TCGA-78-7154 TCGA-78-8662 TCGA-86-7711 TCGA-86-7953 TCGA-86-8074 TCGA-86-8075 
        1948         1964          630          591           24          479 
TCGA-86-8278 TCGA-86-8358 TCGA-86-8669 TCGA-86-8673 TCGA-91-6828 TCGA-91-6830 
         476           19           34          455          323           60 
TCGA-91-6835 TCGA-95-7043 TCGA-95-7947 TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 
          79            2          477          287          116            6 
TCGA-MP-A4SV TCGA-MP-A4TF 
        1946         1970 

$`3Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          426         1126         1947         1431          578 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
         610         1997          455          365          669          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5715 
         761          761          730          457          151           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
          14          225          182         1952         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         864         1073          354         1357          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
        1301           97         1130         1163          190          722 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 
         863          383          723          302          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         705         1938         1942         1864         1978          444 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 
         366          218          557         1970          535          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F 
         385           99          260          486          466          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         351          415           76         1932         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         428          999          896          157         1700          445 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         890          522          354         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
         785          944         1499          282         1091         2370 
TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         653          883          764         1015          255          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 
        1986         1971          424          701         1479         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
          87            2          993           24         1239           25 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
          67         1826         1233         2151         1170           18 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          35          121            6            4           95           40 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
          39           34           24           54           16          197 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          21            3           31           21          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
          43           26            4           47           15           46 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          66          216           44           23           29           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
           8           15          228            9            3          146 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         202           15           48           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          33           42           29            1           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
          47          162         1216         1289         1970         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
        1445         2067         2199         1246          910         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
         628         1189         1126         1968         1959           62 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1305          864         1559           31          610          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 
         427          385          174          141          422          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
         690          414          165          230          184           89 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         100           77          129           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
         912          800          467          131           40           38 
TCGA-73-7498 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7147 
         621         1970         1967         1956         1965         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        1944         1093         1963         1202          760         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1961         1963         1221          678          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1950         1934         1937         1965         1972         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1944          327          881         1952          994         1949 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
        1971         1981         1954         1965         1972          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
        1959           11          422         1968         1963          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 
         745           10         1963           13          489          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
          16         1955           26           35           45           18 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
          15          405           10           30           14           39 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1940          310          417          372          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          35          492          197          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 
         218          297          127          186           34          568 
TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         377          476          121          964         1965         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1332          775          181           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        1965           87          147           15          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
         197          271          392          427          459           44 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
         170          154          114          282          238          578 
TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 
         435          285          622          353         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1954         1954         1957         1980         1951         1944 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 1 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             1988              2696 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              478               457 
[1] "2.0 - 1988.0 (478.0)" "1.0 - 2696.0 (457.0)"
[1] "hr=" "1"  
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  3Q GAIN MUTATED         1       21       20        10        11         11
  3Q GAIN WILD-TYPE       3       92      111        33        58         56
                   vv
clus                STAGE IIIB STAGE IV
  3Q GAIN MUTATED            0        3
  3Q GAIN WILD-TYPE         11       20
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                21                92
  STAGE IB                20               111
  STAGE IIA               10                33
  STAGE IIB               11                58
  STAGE IIIA              11                56
  STAGE IIIB               0                11
  STAGE IV                 3                20
[1] 8 2
[1] 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    27  41   6   2
  3Q GAIN WILD-TYPE 116 218  34  16
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              27               116
  T2              41               218
  T3               6                34
  T4               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                 N0  N1 N2+N3
  3Q GAIN MUTATED    48  17    10
  3Q GAIN WILD-TYPE 247  68    62
D6V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                 48               247
  N1                 17                68
  N2+N3              10                62
[1] 3 2
[1] 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 M1B  MX
  3Q GAIN MUTATED    57   3   0   0  17
  3Q GAIN WILD-TYPE 260  15   1   3 102
D6V6, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               57               260
  M1                3                15
  M1A               0                 1
  M1B               0                 3
  MX               17               102
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    41  36
  3Q GAIN WILD-TYPE 207 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     41   36
  3Q GAIN WILD-TYPE  207  178
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              41               207
  MALE                36               178
[1] 2 2
[1] FALSE
D6V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3Q GAIN MUTATED                            2
  3Q GAIN WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3Q GAIN MUTATED                                  18
  3Q GAIN WILD-TYPE                                75
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                   52
  3Q GAIN WILD-TYPE                                                242
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3Q GAIN MUTATED                                            0
  3Q GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  3Q GAIN MUTATED                                               2
  3Q GAIN WILD-TYPE                                            17
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  3Q GAIN MUTATED                                1
  3Q GAIN WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  3Q GAIN MUTATED                                    0
  3Q GAIN WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  3Q GAIN MUTATED                              0                             2
  3Q GAIN WILD-TYPE                            2                            17
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  3Q GAIN MUTATED                                 0
  3Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  3Q GAIN MUTATED                                               0
  3Q GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  3Q GAIN MUTATED                              0
  3Q GAIN WILD-TYPE                            7
D6V9, multiclass
                                                    clus
vv                                                   3Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              52
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   3Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 75
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               242
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     17
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  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     4  73
  3Q GAIN WILD-TYPE  17 368
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4   73
  3Q GAIN WILD-TYPE   17  368
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                4                17
  YES              73               368
[1] 2 2
[1] FALSE
D6V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    53   2   2   4
  3Q GAIN WILD-TYPE 265   9   2  15
D6V12, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              53               265
  R1               2                 9
  R2               2                 2
  RX               4                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  0     0
  3Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                           2    60
  3Q GAIN WILD-TYPE                        24   302
D6V13, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      2                24
  WHITE                                         60               302
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3  52
  3Q GAIN WILD-TYPE   4 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   52
  3Q GAIN WILD-TYPE    4  280
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO              52               280
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    44  19
  4P GAIN WILD-TYPE 277  63
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               63               340 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19                63 
$`4P GAIN MUTATED`
TCGA-05-4432 TCGA-05-5423 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-44-2656 
         761          151         1492          864          354         1429 
TCGA-44-2662 TCGA-44-4112 TCGA-44-5645 TCGA-44-6775 TCGA-44-7661 TCGA-44-A4SU 
        1280          722          383          705          366           76 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 TCGA-55-6712 
         255         1986          424         1178         1479           24 
TCGA-55-7573 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8302 
           4          100           43            4           47           23 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 
          48            1           28         1445         1246         1728 
TCGA-64-1680 TCGA-64-1681 TCGA-69-7980 TCGA-69-8253 TCGA-75-6214 TCGA-75-7027 
        1126         1968          382          100         1970         1956 
TCGA-78-7145 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7163 
        1973         1963          760         1948         1957         1950 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7539 TCGA-78-7542 TCGA-86-7953 
        1937         1965         1972          327         1952          591 
TCGA-86-7955 TCGA-86-8278 TCGA-86-8279 TCGA-86-8669 TCGA-86-A456 TCGA-91-6836 
         508          476          482           34           10          417 
TCGA-91-6848 TCGA-95-7948 TCGA-97-7937 TCGA-97-8179 TCGA-97-8552 TCGA-MN-A4N5 
         224          476          181           15          115          353 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4TF 
        1967         1954         1970 

$`4P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         761          730          457          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
        1962         1147         1073         1357          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 
         133         1324          400         1367          741         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
        1013          863          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
         704          658         1938         1942         1864         1978 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         444          592          218          557         1970          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         535          719          385           99          260          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
         466          287          337          351          415         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        1081         1421          428          999          268          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         157         1700          445          369          890          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         354         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
        1499          246          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
         653          567          883          764          686         1015 
TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1596 TCGA-55-5899 
         105         1971          280          701         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
           2          993         1239           25         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1826         1233         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
         121            6           95           40         1958           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
          39           34           24           54           19           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
         197           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8092 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
          21            6           26           15           33           46 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
          66          216           44           29           11            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
          15          228            9            3          146          202 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         536           15           48           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DF 
          33           42           29         1952            5           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U 
         162         1216         1289         1970         2696         2067 
TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-5774 
        2199          910          628         1189         1686         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
          62         1305          864         1559          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         610          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 TCGA-69-8255 
         230          184           70           89           77          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         214           61         1600          711          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         467          131           40          164           38          621 
TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
         519         1967         1965         1988         1950         1944 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
        1093         1202         1961         1963         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
         215         1940         1934         1949         1944          881 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         994         1949         1971         1981         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1965         1972          824         1959           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
         422         1968         1963          745           10         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8280 TCGA-86-8281 
          13           24          479          489           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
          19           26           35           45           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         455          405           30           14           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
        1940           60          310           79          372          842 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          35          492          197          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         218          297          127          186           34            2 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
         568          377          477          121          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932         1332          775           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 
        1965           87          147          148          197          271 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         392          427          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T2 
         116            6          285          622         1946         1951 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                 2 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             1986              2696 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
              508               455 
[1] "1.0 - 1986.0 (508.0)" "2.0 - 2696.0 (455.0)"
[1] "hr=" "1.3"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  4P GAIN MUTATED         3       14       26         5        13          8
  4P GAIN WILD-TYPE       1       99      105        38        56         59
                   vv
clus                STAGE IIIB STAGE IV
  4P GAIN MUTATED            1        6
  4P GAIN WILD-TYPE         10       17
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  3                 1
  STAGE IA                14                99
  STAGE IB                26               105
  STAGE IIA                5                38
  STAGE IIB               13                56
  STAGE IIIA               8                59
  STAGE IIIB               1                10
  STAGE IV                 6                17
[1] 8 2
[1] 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    19  50   5   2
  4P GAIN WILD-TYPE 124 209  35  16
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              19               124
  T2              50               209
  T3               5                35
  T4               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                 N0  N1 N2+N3
  4P GAIN MUTATED    53  13     9
  4P GAIN WILD-TYPE 242  72    63
D7V5, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0                 53               242
  N1                 13                72
  N2+N3               9                63
[1] 3 2
[1] 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 M1B  MX
  4P GAIN MUTATED    51   5   0   1  18
  4P GAIN WILD-TYPE 266  13   1   2 101
D7V6, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               51               266
  M1                5                13
  M1A               0                 1
  M1B               1                 2
  MX               18               101
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    40  36
  4P GAIN WILD-TYPE 208 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     40   36
  4P GAIN WILD-TYPE  208  178
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              40               208
  MALE                36               178
[1] 2 2
[1] FALSE
D7V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4P GAIN MUTATED                            1
  4P GAIN WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4P GAIN MUTATED                                   9
  4P GAIN WILD-TYPE                                84
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                   59
  4P GAIN WILD-TYPE                                                235
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4P GAIN MUTATED                                            0
  4P GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  4P GAIN MUTATED                                               3
  4P GAIN WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  4P GAIN MUTATED                                1
  4P GAIN WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  4P GAIN MUTATED                                    1
  4P GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  4P GAIN MUTATED                              0                             2
  4P GAIN WILD-TYPE                            2                            17
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  4P GAIN MUTATED                                 0
  4P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  4P GAIN MUTATED                                               0
  4P GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  4P GAIN MUTATED                              0
  4P GAIN WILD-TYPE                            7
D7V9, multiclass
                                                    clus
vv                                                   4P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              59
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   4P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               235
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     17
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  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     2  74
  4P GAIN WILD-TYPE  19 367
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2   74
  4P GAIN WILD-TYPE   19  367
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                2                19
  YES              74               367
[1] 2 2
[1] FALSE
D7V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    53   1   0   3
  4P GAIN WILD-TYPE 265  10   4  16
D7V12, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              53               265
  R1               1                10
  R2               0                 4
  RX               3                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     2
  4P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           3    63
  4P GAIN WILD-TYPE                        23   299
D7V13, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      3                23
  WHITE                                         63               299
[1] 4 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     2  49
  4P GAIN WILD-TYPE   5 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2   49
  4P GAIN WILD-TYPE    5  283
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              49               283
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    27   6
  4Q GAIN WILD-TYPE 294  76
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               33               370 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6                76 
$`4Q GAIN MUTATED`
TCGA-38-4628 TCGA-38-4629 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-6775 
        1492          864         1429         1367         1280          705 
TCGA-44-7661 TCGA-55-6712 TCGA-55-8089 TCGA-55-8091 TCGA-55-8096 TCGA-55-8614 
         366           24          100           43           47          536 
TCGA-55-8615 TCGA-55-A493 TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 TCGA-64-1680 
          15           28         1445         1246         1728         1126 
TCGA-69-7980 TCGA-69-8253 TCGA-75-7027 TCGA-78-7154 TCGA-78-7163 TCGA-78-7542 
         382          100         1956         1948         1950         1952 
TCGA-86-7953 TCGA-86-8278 TCGA-86-A456 TCGA-91-6836 TCGA-91-6848 TCGA-95-7948 
         591          476           10          417          224          476 
TCGA-97-8552 TCGA-MN-A4N5 TCGA-MP-A4T4 
         115          353         1954 

$`4Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
         761          761          730          457          151          882 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
         670           30           62           14          225          182 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 
         264         1952         1962         1147         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 
        1357          448         1971          133         1324          400 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
         741         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1036          190          722         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         723          328          302          845          704          658 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
        1938         1942         1864         1978          444          592 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
         218          557         1970          882          535          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
         385           99          260          486          466          287 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         337          351          415           76         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        1700          445          369          890          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        2174         2146          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         246          282          267         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 
         567          883          764          686         1015          255 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         105         1986         1971          424          280          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        1178         1479         1375           87            2          993 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
        1239           25         1475           67         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        2151         1170           18           35          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40         1958           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
          34           24           54           19           16          197 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          21            3           31            5           33           21 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
           6           26            4           15           33           46 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          66          216           44           23           29           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
           8           15          228            9            3          146 
TCGA-55-8514 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
         202           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 
          42           29           48         1952            1            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
          47          162         1216         1289         1970         2696 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        2067         2199          910          628         1189         1686 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1968         1959           62         1305          864         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         866           31          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         174          141          422          202          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         414          165          230          184           70           89 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
          77          129          214           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         912          800          467          131           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 
          38          621          519         1970         1967         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1973         1988         1950         1944         1093         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1202          760         1957         1961         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
         678          215         1940         1934         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1972         1949         1944          327          881          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
        1949         1971         1981         1954         1964         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
        1972          824         1959           11          630          422 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
        1968         1963          508          745           10         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 
          13           24          479          489          482           16 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
        1955           19           26           35           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 
          18           15          455          405           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323         1940           60          310           79 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         372          842           35          492          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
          36           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK 
          34            2          568          377          477          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         964         1965         1932         1332          775          181 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
          22          107          182         1965           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
          15          148          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         282          238          578          435          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 
         285          622         1946         1967         1951         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1957         1980         1951         1944         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10                 1 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1956              2696 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
              536               456 
[1] "10.0 - 1956.0 (536.0)" "1.0 - 2696.0 (456.0)" 
[1] "hr=" "1.5"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  4Q GAIN MUTATED         2        5       18         1        10          6
  4Q GAIN WILD-TYPE       2      108      113        42        59         61
                   vv
clus                STAGE IIIB STAGE IV
  4Q GAIN MUTATED            0        2
  4Q GAIN WILD-TYPE         11       21
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                 5               108
  STAGE IB                18               113
  STAGE IIA                1                42
  STAGE IIB               10                59
  STAGE IIIA               6                61
  STAGE IIIB               0                11
  STAGE IV                 2                21
[1] 8 2
[1] 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    10  29   5   0
  4Q GAIN WILD-TYPE 133 230  35  18
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1              10               133
  T2              29               230
  T3               5                35
  T4               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                 N0  N1 N2+N3
  4Q GAIN MUTATED    28   9     7
  4Q GAIN WILD-TYPE 267  76    65
D8V5, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0                 28               267
  N1                  9                76
  N2+N3               7                65
[1] 3 2
[1] 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 M1B  MX
  4Q GAIN MUTATED    31   2   0   0  11
  4Q GAIN WILD-TYPE 286  16   1   3 108
D8V6, multiclass
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               31               286
  M1                2                16
  M1A               0                 1
  M1B               0                 3
  MX               11               108
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    22  22
  4Q GAIN WILD-TYPE 226 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     22   22
  4Q GAIN WILD-TYPE  226  192
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              22               226
  MALE                22               192
[1] 2 2
[1] FALSE
D8V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4Q GAIN MUTATED                            0
  4Q GAIN WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4Q GAIN MUTATED                                   4
  4Q GAIN WILD-TYPE                                89
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                   36
  4Q GAIN WILD-TYPE                                                258
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4Q GAIN MUTATED                                            0
  4Q GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  4Q GAIN MUTATED                                               2
  4Q GAIN WILD-TYPE                                            17
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  4Q GAIN MUTATED                                0
  4Q GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  4Q GAIN MUTATED                                    0
  4Q GAIN WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  4Q GAIN MUTATED                              0                             1
  4Q GAIN WILD-TYPE                            2                            18
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  4Q GAIN MUTATED                                 0
  4Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  4Q GAIN MUTATED                                               1
  4Q GAIN WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  4Q GAIN MUTATED                              0
  4Q GAIN WILD-TYPE                            7
D8V9, multiclass
                                                    clus
vv                                                   4Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              36
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   4Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               258
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     18
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  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  43
  4Q GAIN WILD-TYPE  20 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   43
  4Q GAIN WILD-TYPE   20  398
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1                20
  YES              43               398
[1] 2 2
[1] FALSE
D8V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    31   0   0   2
  4Q GAIN WILD-TYPE 287  11   4  17
D8V12, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              31               287
  R1               0                11
  R2               0                 4
  RX               2                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     1
  4Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           2    34
  4Q GAIN WILD-TYPE                        24   328
D8V13, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      2                24
  WHITE                                         34               328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  30
  4Q GAIN WILD-TYPE   6 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   30
  4Q GAIN WILD-TYPE    6  302
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              30               302
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   177  45
  5P GAIN WILD-TYPE 144  37
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              222               181 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               45                37 
$`5P GAIN MUTATED`
TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4422 TCGA-05-4424 
        1431          610         1958         1997          365          913 
TCGA-05-4426 TCGA-05-4430 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-3615 
         791          761          151          882          670           14 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 
         264         1962         1147         1492          864          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
        1357          448         1971         1429          400         1367 
TCGA-44-2662 TCGA-44-2668 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
        1280          246         1163          190          722          863 
TCGA-44-5645 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
         383          845          658          705         1942         1864 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         444          592          218          557         1970          882 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47F TCGA-44-A4SS 
         719          385           99          466          337          415 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
        1421          428          896          157         1700          369 
TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
         890          354         2174         2146          455          944 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 
        1499          282         2370          653          567          686 
TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 
        1015          255         1986         1971          424          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6972 TCGA-55-6980 
        1178         1479           87            2         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1826         1233         1170            6            4           95 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 
        1958           39           39           34           19          197 
TCGA-55-7911 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8207 
          21           43            4           47           46           66 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
          44           23           11            8           15          228 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
           9          202          536           15           48           66 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
          33           42           29           48         1952           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8399 TCGA-62-8402 
           5           47          162         1216         2696         1445 
TCGA-62-A46U TCGA-62-A471 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 
        2067         1246         1686         1126         1959         1305 
TCGA-64-5781 TCGA-67-3770 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
        1559           31          427          174          141          422 
TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-8253 
         202          690          414          165          230          100 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
          61         1600          467          131           40          164 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 TCGA-78-7147 TCGA-78-7149 TCGA-78-7153 
         519         1970         1965         1950         1093          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
        1948         1957         1221         1950         1934         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 
        1972         1949          327          994         1949         1981 
TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7953 
        1964         1972          824         1959          630          591 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 
         745           10           13          479          482           16 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4D0 
          19           26           35           15          455           30 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-8499 TCGA-91-A4BC 
         323           60          417          372           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 
         218          297          127          186           34          568 
TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 
         477          476          964         1965         1332          775 
TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 
         181          182         1965          148          115          271 
TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
         427          170          154          287          282          578 
TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
           6          353         1967         1951         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        1957         1951         1944         1970          142         1971 

$`5P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 TCGA-05-4427 TCGA-05-4432 
         578          455          912          669          791          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
         730          457           30           62          225          182 
TCGA-38-4625 TCGA-38-4630 TCGA-38-A44F TCGA-44-2655 TCGA-44-2661 TCGA-44-2665 
        1952         1073          133         1324          741         1301 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3918 TCGA-44-5643 TCGA-44-6144 TCGA-44-6145 
          97         1130         1036         1013          723          328 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-6779 TCGA-44-7661 TCGA-44-7671 
         302          704         1938         1978          366          535 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 
         260          486          287          351           76         1932 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-6742 TCGA-49-6745 TCGA-50-5055 
        1081          999          268          445          522          785 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5942 TCGA-50-5944 TCGA-50-8460 
         246          267         1091          883          764          105 
TCGA-53-A4EZ TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
         280         1375          993           24         1239           25 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7728 
        2151           18           35          121           40           24 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
          54           16            3           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8097 TCGA-55-8205 
          21          100            6           26           15           33 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 
         216           29            3          146           49          106 
TCGA-55-A492 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 
           1         1289         1970         2199          910         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 
         628         1189         1968           62          864          866 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 TCGA-69-7974 TCGA-69-7978 
         610          573          385          186          184           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 
          89          382           77          129          214          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4677 TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 
         912          800           38          621         1967         1956 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 
        1973         1988         1944         1963         1202         1961 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 
        1963          678          215         1940         1937         1944 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 TCGA-86-7701 
         881         1952         1971         1954         1965           11 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8074 
         422         1968         1963          508         1963           24 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
         489          476         1955           45           34           18 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6831 
         405           10           14           39         1940          310 
TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
          79          842          224           35          492          197 
TCGA-91-8497 TCGA-95-7043 TCGA-95-7944 TCGA-95-A4VK TCGA-97-7552 TCGA-97-7941 
         174            2          377          121         1932           22 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M2 TCGA-99-7458 
         107           87          147           15          197          392 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
         459           44          114          238          435          116 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TI 
         285          622         1946         1980         1970         1955 
TCGA-MP-A5C7 
        1490 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                 1 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             2696              2199 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            476.5             455.0 
[1] "2.0 - 2696.0 (476.5)" "1.0 - 2199.0 (455.0)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  5P GAIN MUTATED         3       60       76        29        31         34
  5P GAIN WILD-TYPE       1       53       55        14        38         33
                   vv
clus                STAGE IIIB STAGE IV
  5P GAIN MUTATED            8       12
  5P GAIN WILD-TYPE          3       11
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  3                 1
  STAGE IA                60                53
  STAGE IB                76                55
  STAGE IIA               29                14
  STAGE IIB               31                38
  STAGE IIIA              34                33
  STAGE IIIB               8                 3
  STAGE IV                12                11
[1] 8 2
[1] 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    82 147  15   8
  5P GAIN WILD-TYPE  61 112  25  10
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              82                61
  T2             147               112
  T3              15                25
  T4               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                 N0  N1 N2+N3
  5P GAIN MUTATED   159  46    41
  5P GAIN WILD-TYPE 136  39    31
D9V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                159               136
  N1                 46                39
  N2+N3              41                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  5P GAIN MUTATED   167   9   0   2  72
  5P GAIN WILD-TYPE 150   9   1   1  47
D9V6, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              167               150
  M1                9                 9
  M1A               0                 1
  M1B               2                 1
  MX               72                47
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   145 108
  5P GAIN WILD-TYPE 103 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    145  108
  5P GAIN WILD-TYPE  103  106
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE             145               103
  MALE               108               106
[1] 2 2
[1] FALSE
D9V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5P GAIN MUTATED                            6
  5P GAIN WILD-TYPE                          7
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5P GAIN MUTATED                                  46
  5P GAIN WILD-TYPE                                47
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                  172
  5P GAIN WILD-TYPE                                                122
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5P GAIN MUTATED                                            1
  5P GAIN WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  5P GAIN MUTATED                                              10
  5P GAIN WILD-TYPE                                             9
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  5P GAIN MUTATED                                2
  5P GAIN WILD-TYPE                              0
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  5P GAIN MUTATED                                    3
  5P GAIN WILD-TYPE                                  1
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  5P GAIN MUTATED                              0                             9
  5P GAIN WILD-TYPE                            2                            10
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  5P GAIN MUTATED                                 0
  5P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  5P GAIN MUTATED                                               2
  5P GAIN WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  5P GAIN MUTATED                              2
  5P GAIN WILD-TYPE                            5
D9V9, multiclass
                                                    clus
vv                                                   5P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             172
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    9
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   5P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 47
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               122
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      9
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     10
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  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    14 239
  5P GAIN WILD-TYPE   7 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     14  239
  5P GAIN WILD-TYPE    7  202
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               14                 7
  YES             239               202
[1] 2 2
[1] FALSE
D9V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED   178   5   1  10
  5P GAIN WILD-TYPE 140   6   3   9
D9V12, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0             178               140
  R1               5                 6
  R2               1                 3
  RX              10                 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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  1     3
  5P GAIN WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          14   204
  5P GAIN WILD-TYPE                        12   158
D9V13, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 3
  BLACK OR AFRICAN AMERICAN                     14                12
  WHITE                                        204               158
[1] 4 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     4 188
  5P GAIN WILD-TYPE   3 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4  188
  5P GAIN WILD-TYPE    3  144
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             188               144
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    76  22
  5Q GAIN WILD-TYPE 245  60
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               98               305 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               22                60 
$`5Q GAIN MUTATED`
TCGA-05-4398 TCGA-05-4426 TCGA-05-5423 TCGA-35-3615 TCGA-38-6178 TCGA-38-7271 
        1431          791          151           14          448         1971 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-3398 
        1429          400         1367         1280         1301         1163 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6774 TCGA-44-6777 TCGA-44-7659 TCGA-44-7672 
         722          383          658         1942          444          719 
TCGA-44-8119 TCGA-44-A47A TCGA-44-A47F TCGA-49-4501 TCGA-49-4512 TCGA-49-6743 
          99          466          337         1421          157          369 
TCGA-49-6761 TCGA-50-5051 TCGA-50-5935 TCGA-50-6597 TCGA-53-7626 TCGA-53-7813 
         354          455          653         1015         1971          424 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-7573 
        1479            2         1475           67         1826            4 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7910 TCGA-55-7911 TCGA-55-8091 TCGA-55-8206 
          95         1958          197           21           43           46 
TCGA-55-8207 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-A48Z TCGA-55-A493 
          66           15          202          536           29           28 
TCGA-55-A4DG TCGA-62-A46U TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-67-6215 
         162         2067         1126           62         1559          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-8253 TCGA-73-4670 
         141          422          202          690          100          131 
TCGA-73-4675 TCGA-75-6214 TCGA-78-7147 TCGA-78-7153 TCGA-78-7154 TCGA-78-7163 
          40         1970         1950          760         1948         1950 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-80-5608 
        1965         1972         1949          327          994         1972 
TCGA-83-5908 TCGA-86-7711 TCGA-86-8055 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
         824          630           10           16           19           26 
TCGA-86-A4D0 TCGA-91-6836 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7947 
          30          417          218          297          127          477 
TCGA-97-7546 TCGA-97-7547 TCGA-97-8172 TCGA-97-8174 TCGA-97-8552 TCGA-97-A4M7 
         964         1965          182         1965          115          271 
TCGA-J2-A4AE TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TF 
         282         1951         1954         1954         1957         1970 
TCGA-MP-A4TH TCGA-MP-A4TK 
         142         1971 

$`5Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         365          913          669          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         730          457          882          670           30           62 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
         225          182          264         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-A44F 
        1492          864         1073          354         1357          133 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 
        1324          741           97          246         1130         1036 
TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
         190         1013          863          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 
         845          704          705         1938         1864         1978 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         592          366          218          557         1970          882 
TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G 
         535          385          260          486          287          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
         415           76         1932         1081          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
         268          896         1700          445          890          522 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2174         2146          785          944         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 TCGA-50-5942 
         282          267         1091         2370          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-A4EZ 
         764          686          255          105         1986          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
         701         1178         1375           87          993           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
        1239           25         1233         2151         1170           18 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 
          35          121            6           40           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7914 
          34           24           54           19           16            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33           21          100            6 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8299 
          26            4           47           15           33          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
          44           23           29           11            8          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
           9            3          146           15           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 
          66          106           33           42           48         1952 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           1            5           47         1216         1289         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
        2696         1445         2199         1246          910         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
         628         1189         1686         1968         1959         1305 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
         864          866           31          610          573          427 
TCGA-67-3774 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         385          186          414          165          230          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          70           89          382           77          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
          61         1600          711          912          800          467 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7027 
         164           38          621          519         1967         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1965         1973         1988         1944         1093         1963 
TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
        1202         1957         1961         1963         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 
         215         1940         1934         1937         1944          881 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
        1952         1949         1971         1981         1954         1964 
TCGA-80-5607 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        1965         1959           11          422         1968          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
        1963          508          745         1963           13           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8585 
         479          489          476          482         1955           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          45           34           18           15          455          405 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          10           14           39          323         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
         310           79          372          842          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 
         492          197          174           36           44          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK 
          34            2          568          377          476          121 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
        1932         1332          775          181           22          107 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-99-7458 
          87          147           15          148          197          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         427          459           44          170          154          114 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         287          238          578          435          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T9 
         285          622          353         1946         1967         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TI TCGA-MP-A5C7 
        1951         1944         1970         1955         1490 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                 1 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2067              2696 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            451.5             476.0 
[1] "2.0 - 2067.0 (451.5)" "1.0 - 2696.0 (476.0)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  5Q GAIN MUTATED         1       26       33        12        13         18
  5Q GAIN WILD-TYPE       3       87       98        31        56         49
                   vv
clus                STAGE IIIB STAGE IV
  5Q GAIN MUTATED            3        6
  5Q GAIN WILD-TYPE          8       17
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                26                87
  STAGE IB                33                98
  STAGE IIA               12                31
  STAGE IIB               13                56
  STAGE IIIA              18                49
  STAGE IIIB               3                 8
  STAGE IV                 6                17
[1] 8 2
[1] 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    34  69   6   3
  5Q GAIN WILD-TYPE 109 190  34  15
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              34               109
  T2              69               190
  T3               6                34
  T4               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                 N0  N1 N2+N3
  5Q GAIN MUTATED    70  18    20
  5Q GAIN WILD-TYPE 225  67    52
D10V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                 70               225
  N1                 18                67
  N2+N3              20                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  5Q GAIN MUTATED    76   6   0   0  28
  5Q GAIN WILD-TYPE 241  12   1   3  91
D10V6, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               76               241
  M1                6                12
  M1A               0                 1
  M1B               0                 3
  MX               28                91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    70  42
  5Q GAIN WILD-TYPE 178 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     70   42
  5Q GAIN WILD-TYPE  178  172
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              70               178
  MALE                42               172
[1] 2 2
[1] FALSE
D10V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5Q GAIN MUTATED                            4
  5Q GAIN WILD-TYPE                          9
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5Q GAIN MUTATED                                  18
  5Q GAIN WILD-TYPE                                75
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                   76
  5Q GAIN WILD-TYPE                                                218
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5Q GAIN MUTATED                                            1
  5Q GAIN WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  5Q GAIN MUTATED                                               5
  5Q GAIN WILD-TYPE                                            14
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  5Q GAIN MUTATED                                2
  5Q GAIN WILD-TYPE                              0
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  5Q GAIN MUTATED                                    0
  5Q GAIN WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  5Q GAIN MUTATED                              0                             4
  5Q GAIN WILD-TYPE                            2                            15
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  5Q GAIN MUTATED                                 0
  5Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  5Q GAIN MUTATED                                               0
  5Q GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  5Q GAIN MUTATED                              2
  5Q GAIN WILD-TYPE                            5
D10V9, multiclass
                                                    clus
vv                                                   5Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              76
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    5
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   5Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 75
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               218
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     14
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     15
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  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     8 104
  5Q GAIN WILD-TYPE  13 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      8  104
  5Q GAIN WILD-TYPE   13  337
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                8                13
  YES             104               337
[1] 2 2
[1] FALSE
D10V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    79   3   1   4
  5Q GAIN WILD-TYPE 239   8   3  15
D10V12, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              79               239
  R1               3                 8
  R2               1                 3
  RX               4                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           5    93
  5Q GAIN WILD-TYPE                        21   269
D10V13, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      5                21
  WHITE                                         93               269
[1] 4 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     1  82
  5Q GAIN WILD-TYPE   6 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   82
  5Q GAIN WILD-TYPE    6  250
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              82               250
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    96  19
  6P GAIN WILD-TYPE 225  63
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              115               288 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               19                63 
$`6P GAIN MUTATED`
TCGA-05-4249 TCGA-05-4410 TCGA-05-4420 TCGA-05-4430 TCGA-05-5425 TCGA-35-3615 
        1523         1958          912          761          882           14 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-44-2659 TCGA-44-3918 TCGA-44-6147 
         264         1952         1492         1367         1036          845 
TCGA-44-6774 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-A4SU TCGA-49-4510 
         658          218          557          882           76          896 
TCGA-49-6742 TCGA-49-6761 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 
         445          354          267         2370          567          764 
TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         686          255         1986          424          280          701 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 TCGA-55-7573 TCGA-55-7903 TCGA-55-7995 
        1479         1375          993            4           19            5 
TCGA-55-8085 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8507 TCGA-55-8511 
          33           15           33           46            8            9 
TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y 
           3          202          536           15           66           42 
TCGA-55-A490 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 TCGA-64-1677 
          48         1970         2696         2199         1246          628 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-67-3771 TCGA-67-3773 TCGA-69-7763 
        1126         1959          864          610          427          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-69-8255 TCGA-71-6725 TCGA-73-4662 
         414          165           89          129           61          912 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 
         467          131           38          621          519         1970 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 
        1950         1093         1957         1221          215         1940 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8655 
        1937         1965          327         1952          994         1981 
TCGA-78-8662 TCGA-86-6851 TCGA-86-7954 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
        1964         1959         1963           24          479          482 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8674 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 
        1955           19          405           79          417          842 
TCGA-91-6848 TCGA-91-8499 TCGA-95-7567 TCGA-95-7944 TCGA-97-7546 TCGA-97-7553 
         224           36          568          377          964         1332 
TCGA-97-8171 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 
         107          147           15          271          427          170 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         114          282            6          622          353         1946 
TCGA-MP-A4TE 
        1970 

$`6P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
         607          426         1369         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
         578          610         1997          455          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         669          791          791          761          730          457 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
         151          670           30           62          225          182 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1962         1147          864         1073          354         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
         448         1971          133         1324         1429          400 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         741         1280         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1163          190          722         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 
         723          328          302          704          705         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
        1942         1864         1978          444          592          366 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
        1970          535          719          385           99          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         486          466          287          337          351          415 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        1932         1081         1421          428          999          268 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 
         157         1700          369          890          522         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2146          455          785          944         1499          246 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 
         282         1091          653          883         1015          105 
TCGA-53-7626 TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 
        1971         1178           87            2           24         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
          25         1475           67         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 
        1170           18           35          121            6           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          54           16          197           21            3           31 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
          21          100            6           43           26            4 
TCGA-55-8096 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          47           66          216           44           23           29 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 
          11           15          228          146           48           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
         106           33           29         1952            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 
           5           47          162         1216         1289         1445 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
        2067          910         1728         1189         1686         1968 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 
          62         1305         1559          866           31          573 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         230          184           70          382          100           77 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 
         214         1600          711          800           40          164 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
        1967         1956         1965         1973         1988         1944 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
        1963         1202          760         1948         1961         1963 
TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
         678         1950         1934         1972         1949         1944 
TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 
         881         1949         1971         1954         1965         1972 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
         824           11          630          422         1968          591 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
         508          745           10         1963           13          489 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
         476           16           26           35           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          18           15          455           10           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 
          39          323         1940           60          310          372 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
          35          492          197          174           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7947 
         297          127          186           34            2          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 
         476          121         1965         1932          775          181 
TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8547 TCGA-97-8552 
          22          182         1965           87          148          115 
TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-A4AD 
         197          392          459           44          154          287 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MP-A4SW 
         238          578          435          116          285         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1951         1954         1954         1957         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1944         1970          142         1955         1971         1490 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                 1 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             2696              2174 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              536               455 
[1] "3.0 - 2696.0 (536.0)" "1.0 - 2174.0 (455.0)"
[1] "hr=" "1.5"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  6P GAIN MUTATED         1       40       34        10        15         17
  6P GAIN WILD-TYPE       3       73       97        33        54         50
                   vv
clus                STAGE IIIB STAGE IV
  6P GAIN MUTATED            4       10
  6P GAIN WILD-TYPE          7       13
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                40                73
  STAGE IB                34                97
  STAGE IIA               10                33
  STAGE IIB               15                54
  STAGE IIIA              17                50
  STAGE IIIB               4                 7
  STAGE IV                10                13
[1] 8 2
[1] 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    47  70   8   5
  6P GAIN WILD-TYPE  96 189  32  13
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              47                96
  T2              70               189
  T3               8                32
  T4               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                 N0  N1 N2+N3
  6P GAIN MUTATED    88  18    21
  6P GAIN WILD-TYPE 207  67    51
D11V5, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0                 88               207
  N1                 18                67
  N2+N3              21                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  6P GAIN MUTATED    89   6   1   2  33
  6P GAIN WILD-TYPE 228  12   0   1  86
D11V6, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               89               228
  M1                6                12
  M1A               1                 0
  M1B               2                 1
  MX               33                86
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    69  62
  6P GAIN WILD-TYPE 179 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     69   62
  6P GAIN WILD-TYPE  179  152
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              69               179
  MALE                62               152
[1] 2 2
[1] FALSE
D11V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6P GAIN MUTATED                            7
  6P GAIN WILD-TYPE                          6
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6P GAIN MUTATED                                  27
  6P GAIN WILD-TYPE                                66
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                   80
  6P GAIN WILD-TYPE                                                214
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6P GAIN MUTATED                                            0
  6P GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  6P GAIN MUTATED                                               6
  6P GAIN WILD-TYPE                                            13
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  6P GAIN MUTATED                                1
  6P GAIN WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  6P GAIN MUTATED                                    1
  6P GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  6P GAIN MUTATED                              0                             7
  6P GAIN WILD-TYPE                            2                            12
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  6P GAIN MUTATED                                 0
  6P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  6P GAIN MUTATED                                               1
  6P GAIN WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  6P GAIN MUTATED                              1
  6P GAIN WILD-TYPE                            6
D11V9, multiclass
                                                    clus
vv                                                   6P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              80
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    6
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    7
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   6P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               214
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     13
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     12
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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     5 126
  6P GAIN WILD-TYPE  16 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5  126
  6P GAIN WILD-TYPE   16  315
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                5                16
  YES             126               315
[1] 2 2
[1] FALSE
D11V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    92   2   0   5
  6P GAIN WILD-TYPE 226   9   4  14
D11V12, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              92               226
  R1               2                 9
  R2               0                 4
  RX               5                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  1     4
  6P GAIN WILD-TYPE                                0     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           5   110
  6P GAIN WILD-TYPE                        21   252
D11V13, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 2
  BLACK OR AFRICAN AMERICAN                      5                21
  WHITE                                        110               252
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     4  97
  6P GAIN WILD-TYPE   3 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4   97
  6P GAIN WILD-TYPE    3  235
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO              97               235
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    43   5
  6Q GAIN WILD-TYPE 278  77
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               355 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                77 
$`6Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4420 TCGA-05-4432 TCGA-05-5425 TCGA-35-5375 TCGA-38-4625 
        1523          912          761          882          264         1952 
TCGA-38-4628 TCGA-44-7667 TCGA-44-7670 TCGA-49-6742 TCGA-50-6597 TCGA-50-7109 
        1492          557          882          445         1015          255 
TCGA-53-A4EZ TCGA-55-1596 TCGA-55-7910 TCGA-55-7995 TCGA-55-8097 TCGA-55-8206 
         280         1375          197            5           15           46 
TCGA-55-8507 TCGA-55-8511 TCGA-55-8514 TCGA-55-8620 TCGA-62-A471 TCGA-67-3773 
           8            9          202           66         1246          427 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-71-6725 TCGA-73-4677 
         690          414          165           89           61           38 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-8662 TCGA-86-6851 TCGA-86-7954 
        1937         1965          327         1964         1959         1963 
TCGA-86-8074 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-95-7944 
          24          417          842          224           36          377 
TCGA-97-7546 TCGA-97-8177 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AE TCGA-MN-A4N4 
         964          147          427          170          282          622 

$`6Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
         607          426         1369         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
         578          610         1958         1997          455          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
         913          669          791          791          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         457          151          670           30           62           14 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 
         225          182         1962         1147          864         1073 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
         354         1357          448         1971          133         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1429          400         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
         722         1013          863          383          723          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          845          704          658          705         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
        1942         1864         1978          444          592          366 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
         218         1970          535          719          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
         260          486          466          287          337          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         415           76         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
         999          268          896          157         1700          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         890          522          354         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         785          944         1499          246          282          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 
         686          105         1986         1971          424          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        1178         1479           87            2          993           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
        1239           25         1475           67         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        2151         1170           18           35          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40         1958           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
          34           24           54           19           16           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
           3           31           33           21          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8207 
          43           26            4           47           33           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
         216           44           23           29           11           15 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
         228            3          146          536           15           48 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          49          106           33           42           29           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1952            1           28            5           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U 
        1216         1289         1970         2696         1445         2067 
TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        2199          910         1728          628         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1126         1968         1959           62         1305          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 
        1559          866           31          610          573          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 
         174          141          422          202          186          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
         184           70          382          100           77          129 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
         214         1600          711          912          800          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 
         131           40          164          621          519         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1967         1956         1965         1973         1988         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1944         1093         1963         1202          760         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1957         1961         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        1940         1950         1934         1972         1949         1944 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881         1952          994         1949         1971         1981 
TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 
        1954         1965         1972          824           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
         422         1968          591          508          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        1963           13          479          489          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
          16         1955           19           26           35           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          34           18           15          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          30           14           39          323         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         310           79          372           35          492          197 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
         174           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
          34            2          568          477          476          121 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
        1965         1932         1332          775          181           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 
         107          182         1965           87           15          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
         115          197          271          392          459           44 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         154          114          287          238          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         116            6          285          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1951         1954         1954         1957         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1944         1970         1970          142         1955         1971 
TCGA-MP-A5C7 
        1490 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                 1 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             1965              2696 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            415.5             477.0 
[1] "5.0 - 1965.0 (415.5)" "1.0 - 2696.0 (477.0)"
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  6Q GAIN MUTATED         1       13       16         6         8          6
  6Q GAIN WILD-TYPE       3      100      115        37        61         61
                   vv
clus                STAGE IIIB STAGE IV
  6Q GAIN MUTATED            1        5
  6Q GAIN WILD-TYPE         10       18
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                13               100
  STAGE IB                16               115
  STAGE IIA                6                37
  STAGE IIB                8                61
  STAGE IIIA               6                61
  STAGE IIIB               1                10
  STAGE IV                 5                18
[1] 8 2
[1] 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  32   4   2
  6Q GAIN WILD-TYPE 126 227  36  16
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              17               126
  T2              32               227
  T3               4                36
  T4               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                 N0  N1 N2+N3
  6Q GAIN MUTATED    37  11     7
  6Q GAIN WILD-TYPE 258  74    65
D12V5, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0                 37               258
  N1                 11                74
  N2+N3               7                65
[1] 3 2
[1] 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 M1B  MX
  6Q GAIN MUTATED    36   3   0   1  16
  6Q GAIN WILD-TYPE 281  15   1   2 103
D12V6, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               36               281
  M1                3                15
  M1A               0                 1
  M1B               1                 2
  MX               16               103
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    32  24
  6Q GAIN WILD-TYPE 216 190
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     32   24
  6Q GAIN WILD-TYPE  216  190
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              32               216
  MALE                24               190
[1] 2 2
[1] FALSE
D12V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6Q GAIN MUTATED                            3
  6Q GAIN WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6Q GAIN MUTATED                                  12
  6Q GAIN WILD-TYPE                                81
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                   37
  6Q GAIN WILD-TYPE                                                257
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6Q GAIN MUTATED                                            0
  6Q GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  6Q GAIN MUTATED                                               1
  6Q GAIN WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  6Q GAIN MUTATED                                0
  6Q GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  6Q GAIN MUTATED                                    0
  6Q GAIN WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  6Q GAIN MUTATED                              0                             2
  6Q GAIN WILD-TYPE                            2                            17
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  6Q GAIN MUTATED                                 0
  6Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  6Q GAIN MUTATED                                               0
  6Q GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  6Q GAIN MUTATED                              1
  6Q GAIN WILD-TYPE                            6
D12V9, multiclass
                                                    clus
vv                                                   6Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               12
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              37
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   6Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               257
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     17
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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     1  55
  6Q GAIN WILD-TYPE  20 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   55
  6Q GAIN WILD-TYPE   20  386
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                1                20
  YES              55               386
[1] 2 2
[1] FALSE
D12V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    38   0   0   3
  6Q GAIN WILD-TYPE 280  11   4  16
D12V12, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              38               280
  R1               0                11
  R2               0                 4
  RX               3                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     2
  6Q GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           4    44
  6Q GAIN WILD-TYPE                        22   318
D12V13, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      4                22
  WHITE                                         44               318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  42
  6Q GAIN WILD-TYPE   5 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   42
  6Q GAIN WILD-TYPE    5  290
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              42               290
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   166  38
  7P GAIN WILD-TYPE 155  44
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              204               199 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               38                44 
$`7P GAIN MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 
         607         1369         1126         1431          610         1958 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
        1997          455          912          151          882          670 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
         225          182          264         1952         1147         1492 
TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 
         864          354         1357          448         1429          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-3396 TCGA-44-3919 TCGA-44-4112 
        1367          741         1280         1130          190          722 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6147 TCGA-44-6775 TCGA-44-6777 
         863          383          723          845          705         1942 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
        1978          592          366          218          557         1970 
TCGA-44-8117 TCGA-44-A479 TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 
         385          486          337          415           76         1081 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-6745 TCGA-49-6761 
         428          999          896          157          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5933 
        2174         2146          785          944          246         2370 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-55-1596 
         567          764          686         1015         1986         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
          87            2           24           25         1475           67 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7724 
        1233         1170           35          121           40         1958 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-8085 
          39           34           16          197           31           33 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 
          43           26           47           33           46           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 
          23           29          228            9          202           15 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
          48           66           29           48         1952            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
          28            5          162         1289         1970         2696 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 
         910         1728         1686         1126         1968          864 
TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7764 
        1559          610          573          422          202          414 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
         165          184           89          129          214           61 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
        1600          912          467          131           40          164 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 
         519         1970         1967         1973         1950         1963 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 
        1948         1957          678          215         1950         1972 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-7701 
         881         1952         1981         1964          824           11 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 
         422          591          508           10           13           24 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
         479          482           16           19           26           45 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6831 TCGA-91-6835 
          15          455           10           14          310           79 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-A4BC TCGA-93-7348 TCGA-95-7567 
         842          224          197           44          127          568 
TCGA-95-7944 TCGA-95-7947 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
         377          477         1332          775          181          107 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 
          87          147           15          148          115          271 
TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
         427          170          154          114          287          282 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         578          116            6          285          622          353 
TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TK 
        1951         1957         1980         1951         1944         1971 

$`7P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4422 TCGA-05-4424 
        1523          426         1947          578          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         669          791          791          761          761          730 
TCGA-05-5420 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4630 
         457           30           62           14         1962         1073 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1971          133         1324         1301           97          246 
TCGA-44-3398 TCGA-44-3918 TCGA-44-5643 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
        1163         1036         1013          328          302          704 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 TCGA-44-7670 TCGA-44-7671 
         658         1938         1864          444          882          535 
TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
         719           99          260          466          287          351 
TCGA-49-4486 TCGA-49-4501 TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
        1932         1421          268         1700          445          369 
TCGA-49-6744 TCGA-50-5051 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         890          455         1499          282          267         1091 
TCGA-50-5935 TCGA-50-5942 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
         653          883          255          105         1971          424 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-6642 TCGA-55-6969 
         280          701         1178         1479          993         1239 
TCGA-55-6983 TCGA-55-6986 TCGA-55-7281 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1826         2151           18            6            4           95 
TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 
          39           24           54           19           21            3 
TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8094 TCGA-55-8097 
           5           21          100            6            4           15 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 
          66          216           11            8           15            3 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         146          536           49          106           33           42 
TCGA-55-A4DF TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
          47         1216         1445         2067         2199         1246 
TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 
         628         1189         1959           62         1305          866 
TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 
          31          427          385          174          141          186 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         690          230           70          382          100           77 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 TCGA-75-7031 
         711          800           38          621         1956         1965 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
        1988         1944         1093         1202          760         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        1963         1221         1940         1934         1937         1965 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1949         1944          327          994         1949         1971 
TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 
        1954         1965         1972         1959          630         1968 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 
        1963          745         1963          489          476         1955 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P8 
          35           34           18          405           30           39 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6849 
         323         1940           60          417          372           35 
TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 
         492          174           36          218          297          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
          34            2          476          121          964         1965 
TCGA-97-7552 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-A4M2 TCGA-99-7458 
        1932           22          182         1965          197          392 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4SV TCGA-MP-A4SW 
         459           44          238          435         1946         1967 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1954         1954         1970         1970          142         1955 
TCGA-MP-A5C7 
        1490 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                1                 2 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             2696              2199 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              438               489 
[1] "1.0 - 2696.0 (438.0)" "2.0 - 2199.0 (489.0)"
[1] "hr=" "1.2"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  7P GAIN MUTATED         2       52       70        20        34         43
  7P GAIN WILD-TYPE       2       61       61        23        35         24
                   vv
clus                STAGE IIIB STAGE IV
  7P GAIN MUTATED            6       14
  7P GAIN WILD-TYPE          5        9
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                52                61
  STAGE IB                70                61
  STAGE IIA               20                23
  STAGE IIB               34                35
  STAGE IIIA              43                24
  STAGE IIIB               6                 5
  STAGE IV                14                 9
[1] 8 2
[1] 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    68 139  25   8
  7P GAIN WILD-TYPE  75 120  15  10
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              68                75
  T2             139               120
  T3              25                15
  T4               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                 N0  N1 N2+N3
  7P GAIN MUTATED   142  41    51
  7P GAIN WILD-TYPE 153  44    21
D13V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                142               153
  N1                 41                44
  N2+N3              51                21
[1] 3 2
[1] 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 M1B  MX
  7P GAIN MUTATED   161  11   1   1  64
  7P GAIN WILD-TYPE 156   7   0   2  55
D13V6, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              161               156
  M1               11                 7
  M1A               1                 0
  M1B               1                 2
  MX               64                55
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   131 110
  7P GAIN WILD-TYPE 117 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    131  110
  7P GAIN WILD-TYPE  117  104
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             131               117
  MALE               110               104
[1] 2 2
[1] FALSE
D13V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7P GAIN MUTATED                            5
  7P GAIN WILD-TYPE                          8
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7P GAIN MUTATED                                  42
  7P GAIN WILD-TYPE                                51
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                  166
  7P GAIN WILD-TYPE                                                128
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7P GAIN MUTATED                                            3
  7P GAIN WILD-TYPE                                          1
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  7P GAIN MUTATED                                              10
  7P GAIN WILD-TYPE                                             9
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  7P GAIN MUTATED                                0
  7P GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  7P GAIN MUTATED                                    3
  7P GAIN WILD-TYPE                                  1
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  7P GAIN MUTATED                              0                             8
  7P GAIN WILD-TYPE                            2                            11
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  7P GAIN MUTATED                                 0
  7P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  7P GAIN MUTATED                                               3
  7P GAIN WILD-TYPE                                             1
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  7P GAIN MUTATED                              1
  7P GAIN WILD-TYPE                            6
D13V9, multiclass
                                                    clus
vv                                                   7P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             166
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    8
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   7P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               128
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      9
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     11
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      1
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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     9 232
  7P GAIN WILD-TYPE  12 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9  232
  7P GAIN WILD-TYPE   12  209
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                9                12
  YES             232               209
[1] 2 2
[1] FALSE
D13V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   162   5   3  11
  7P GAIN WILD-TYPE 156   6   1   8
D13V12, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             162               156
  R1               5                 6
  R2               3                 1
  RX              11                 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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     4
  7P GAIN WILD-TYPE                                0     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          16   188
  7P GAIN WILD-TYPE                        10   174
D13V13, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 2
  BLACK OR AFRICAN AMERICAN                     16                10
  WHITE                                        188               174
[1] 4 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     3 177
  7P GAIN WILD-TYPE   4 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3  177
  7P GAIN WILD-TYPE    4  155
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             177               155
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   139  33
  7Q GAIN WILD-TYPE 182  49
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              172               231 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               33                49 
$`7Q GAIN MUTATED`
TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 
        1126         1431          610         1958         1997          912 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         151          882          670          225          182          264 
TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 
        1952         1147         1492         1357          448         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 
         400         1367         1280         1130         1036          190 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6777 TCGA-44-6778 
         383          723          328          845         1942         1864 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-8117 TCGA-44-A47F 
         592          366          218         1970          385          337 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
         415           76         1081          428          999          896 
TCGA-49-4512 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5072 
         157          522         2174         2146          944          246 
TCGA-50-5930 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
         282          653          567          764          686         1015 
TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 
        1986          280          701         1375            2           24 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 
          25         1475           67         1233         1170           35 
TCGA-55-7284 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 
         121           40         1958           39           16          197 
TCGA-55-7994 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 
          31           43           26           47           33           46 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 
          44           23           29            8          228            9 
TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 
         202           48           66           29           48            1 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A472 
          28            5         1289         1970         2696          910 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 
        1728         1686         1126         1968          864         1559 
TCGA-67-3772 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
         573          202          690          414          165          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
          70           89          214           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
         912          800          131           40          164          519 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7160 TCGA-78-7163 TCGA-78-7220 TCGA-78-7540 
        1973         1950          678         1950         1965          881 
TCGA-78-8655 TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 
        1981          824           11          422          591          508 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8280 TCGA-86-8359 TCGA-86-8668 
          10           13          479           16           26           45 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A4P7 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 
          15          455           14           79          842          224 
TCGA-91-8496 TCGA-91-A4BC TCGA-93-7348 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         197           44          127          568          377          477 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 
        1332          775          181          107           87           15 
TCGA-97-8552 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 
         115          427          170          154          287          578 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T8 
           6          285          622         1946         1951         1957 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TK 
        1980         1951         1944         1971 

$`7Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4403 
        1523          607          426         1369         1947          578 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         455          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5429 TCGA-05-5715 
         761          761          730          457           30           62 
TCGA-35-3615 TCGA-38-4626 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 
          14         1962          864         1073          354         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
         133         1324          741         1301           97          246 
TCGA-44-3398 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6146 TCGA-44-6148 
        1163          722         1013          863          302          704 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 
         658          705         1938         1978          444          557 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         882          535          719           99          260          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 TCGA-49-4501 TCGA-49-4507 
         466          287          351         1932         1421          268 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-50-5051 
        1700          445          369          890          354          455 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5942 
         785         1499          267         1091         2370          883 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 
         255          105         1971          424         1178         1479 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6969 TCGA-55-6983 TCGA-55-6986 TCGA-55-7281 
          87          993         1239         1826         2151           18 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
           6            4           95           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
          54           19           21            3            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8094 TCGA-55-8097 TCGA-55-8207 
          21          100            6            4           15           66 
TCGA-55-8299 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
         216           11           15            3          146          536 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A491 
          15           49          106           33           42         1952 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
          47          162         1216         1445         2067         2199 
TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1246          628         1189         1959           62         1305 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
         866           31          610          427          385          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 
         141          422          186          230          382          100 
TCGA-69-8254 TCGA-69-8255 TCGA-73-4668 TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 
          77          129          467           38          621         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
        1967         1956         1965         1988         1944         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1963         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
        1963         1221          215         1940         1934         1937 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 
        1972         1949         1944          327         1952          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1949         1971         1954         1964         1965         1972 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 
        1959          630         1968         1963          745         1963 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 
          24          489          476          482         1955           19 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          35           34           18          405           10           30 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
          39          323         1940           60          310          417 
TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
         372           35          492          174           36          218 
TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VK 
         297          186           34            2          476          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 
         964         1965         1932           22          182         1965 
TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
         147          148          197          271          392          459 
TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
          44          114          282          238          435          116 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF 
         353         1967         1954         1954         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
         142         1955         1490 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                 2 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             2696              2370 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              438               476 
[1] "1.0 - 2696.0 (438.0)" "2.0 - 2370.0 (476.0)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  7Q GAIN MUTATED         2       45       52        17        27         37
  7Q GAIN WILD-TYPE       2       68       79        26        42         30
                   vv
clus                STAGE IIIB STAGE IV
  7Q GAIN MUTATED            5       14
  7Q GAIN WILD-TYPE          6        9
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                45                68
  STAGE IB                52                79
  STAGE IIA               17                26
  STAGE IIB               27                42
  STAGE IIIA              37                30
  STAGE IIIB               5                 6
  STAGE IV                14                 9
[1] 8 2
[1] 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    57 116  18   7
  7Q GAIN WILD-TYPE  86 143  22  11
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              57                86
  T2             116               143
  T3              18                22
  T4               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                 N0  N1 N2+N3
  7Q GAIN MUTATED   115  34    43
  7Q GAIN WILD-TYPE 180  51    29
D14V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                115               180
  N1                 34                51
  N2+N3              43                29
[1] 3 2
[1] 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 M1B  MX
  7Q GAIN MUTATED   130  11   1   1  54
  7Q GAIN WILD-TYPE 187   7   0   2  65
D14V6, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              130               187
  M1               11                 7
  M1A               1                 0
  M1B               1                 2
  MX               54                65
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   106  93
  7Q GAIN WILD-TYPE 142 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    106   93
  7Q GAIN WILD-TYPE  142  121
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             106               142
  MALE                93               121
[1] 2 2
[1] FALSE
D14V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7Q GAIN MUTATED                            6
  7Q GAIN WILD-TYPE                          7
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7Q GAIN MUTATED                                  37
  7Q GAIN WILD-TYPE                                56
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                  135
  7Q GAIN WILD-TYPE                                                159
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7Q GAIN MUTATED                                            3
  7Q GAIN WILD-TYPE                                          1
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  7Q GAIN MUTATED                                              10
  7Q GAIN WILD-TYPE                                             9
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  7Q GAIN MUTATED                                0
  7Q GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  7Q GAIN MUTATED                                    1
  7Q GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  7Q GAIN MUTATED                              0                             6
  7Q GAIN WILD-TYPE                            2                            13
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  7Q GAIN MUTATED                                 0
  7Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  7Q GAIN MUTATED                                               1
  7Q GAIN WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  7Q GAIN MUTATED                              0
  7Q GAIN WILD-TYPE                            7
D14V9, multiclass
                                                    clus
vv                                                   7Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             135
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    6
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   7Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               159
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      9
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     13
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  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    12 187
  7Q GAIN WILD-TYPE   9 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     12  187
  7Q GAIN WILD-TYPE    9  254
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               12                 9
  YES             187               254
[1] 2 2
[1] FALSE
D14V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   129   4   3  10
  7Q GAIN WILD-TYPE 189   7   1   9
D14V12, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             129               189
  R1               4                 7
  R2               3                 1
  RX              10                 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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     3
  7Q GAIN WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          14   160
  7Q GAIN WILD-TYPE                        12   202
D14V13, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 3
  BLACK OR AFRICAN AMERICAN                     14                12
  WHITE                                        160               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"
D14V14, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2 153
  7Q GAIN WILD-TYPE   5 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  153
  7Q GAIN WILD-TYPE    5  179
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             153               179
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    79  21
  8P GAIN WILD-TYPE 242  61
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              100               303 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               21                61 
$`8P GAIN MUTATED`
TCGA-05-4405 TCGA-05-4417 TCGA-05-4424 TCGA-05-4432 TCGA-05-5428 TCGA-35-5375 
         610          455          913          761          670          264 
TCGA-38-4625 TCGA-38-4629 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-6147 
        1952          864         1357          448         1429          845 
TCGA-44-6778 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
        1864          557         1970          535          719           99 
TCGA-44-8120 TCGA-44-A47B TCGA-44-A47F TCGA-49-4512 TCGA-49-6742 TCGA-50-5051 
         260          287          337          157          445          455 
TCGA-50-5072 TCGA-50-5933 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-55-1592 
         246         2370          764          686          255          701 
TCGA-55-1596 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-7574 TCGA-55-7724 
        1375         1239           25         1475           95         1958 
TCGA-55-7907 TCGA-55-8096 TCGA-55-8206 TCGA-55-8301 TCGA-55-8507 TCGA-55-8614 
          16           47           46           44            8          536 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A494 TCGA-62-8398 
          15           66           29           48            5         1970 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 TCGA-64-5779 TCGA-69-7763 
        1246          910          628         1126          864          690 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
         414          230          184          214           61         1600 
TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-7027 
         711          131           40          164           38         1956 
TCGA-75-7031 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7158 TCGA-78-7159 
        1965         1944         1093          760         1963         1221 
TCGA-78-7535 TCGA-80-5607 TCGA-86-7701 TCGA-86-8280 TCGA-86-8585 TCGA-86-8669 
        1972         1965           11           16           35           34 
TCGA-86-8674 TCGA-91-6828 TCGA-91-6831 TCGA-91-6840 TCGA-91-7771 TCGA-93-7347 
         405          323          310          372          492          297 
TCGA-95-7567 TCGA-95-7948 TCGA-97-7547 TCGA-97-7553 TCGA-97-8172 TCGA-97-8552 
         568          476         1965         1332          182          115 
TCGA-97-A4M2 TCGA-99-8025 TCGA-99-8033 TCGA-L9-A444 TCGA-MP-A4T2 TCGA-MP-A4T8 
         197          427          170            6         1951         1957 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1951         1970         1970          142 

$`8P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 
        1431          578         1958         1997          912          365 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 
         669          791          791          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         151          882           30           62           14          225 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 
         182         1962         1147         1492         1073          354 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        1971          133         1324          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1036          190          722         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         723          328          302          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
        1938         1942         1978          444          592          366 
TCGA-44-7662 TCGA-44-7670 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G 
         218          882          385          486          466          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         415           76         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
         999          268          896         1700          369          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         522          354         2174         2146          785          944 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 
        1499          282          267         1091          653          567 
TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
         883         1015          105         1986         1971          424 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         280         1178         1479           87            2          993 
TCGA-55-6712 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
          24           67         1826         1233         2151         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 
          18           35          121            6            4           40 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
          39           39           34           24           54           19 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
         197           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
          21          100            6           43           26            4 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 
          15           33           66          216           23           29 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          11           15          228            9            3          146 
TCGA-55-8514 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         202           48           49          106           33           42 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
        1952            1           28           47          162         1216 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-64-1676 
        1289         2696         1445         2067         2199         1728 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1189         1686         1968         1959           62         1305 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        1559          866           31          610          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         165           70           89          382          100           77 
TCGA-69-8255 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-7498 TCGA-73-7499 
         129          912          800          467          621          519 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 
        1970         1967         1973         1988         1950         1963 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 
        1202         1948         1957         1961          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        1940         1950         1934         1937         1965         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1944          327          881         1952          994         1949 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 
        1971         1981         1954         1964         1972          824 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        1959          630          422         1968          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
         508          745           10         1963           13           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 
         479          489          476          482         1955           19 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 
          26           45           18           15          455           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
          30           14           39         1940           60           79 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
         417          842          224           35          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 
          36           44          218          127          186           34 
TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 
           2          377          477          121          964         1932 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
         775          181           22          107         1965           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
         147           15          148          271          392          459 
TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
          44          154          114          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         578          435          116          285          622          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC 
        1946         1967         1954         1954         1980         1944 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                 1 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             2370              2696 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              484               459 
[1] "5.0 - 2370.0 (484.0)" "1.0 - 2696.0 (459.0)"
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  8P GAIN MUTATED         2       22       37        10        17         17
  8P GAIN WILD-TYPE       2       91       94        33        52         50
                   vv
clus                STAGE IIIB STAGE IV
  8P GAIN MUTATED            4        6
  8P GAIN WILD-TYPE          7       17
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                22                91
  STAGE IB                37                94
  STAGE IIA               10                33
  STAGE IIB               17                52
  STAGE IIIA              17                50
  STAGE IIIB               4                 7
  STAGE IV                 6                17
[1] 8 2
[1] 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    26  73  12   3
  8P GAIN WILD-TYPE 117 186  28  15
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              26               117
  T2              73               186
  T3              12                28
  T4               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                 N0  N1 N2+N3
  8P GAIN MUTATED    74  19    19
  8P GAIN WILD-TYPE 221  66    53
D15V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                 74               221
  N1                 19                66
  N2+N3              19                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  8P GAIN MUTATED    79   5   0   1  29
  8P GAIN WILD-TYPE 238  13   1   2  90
D15V6, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               79               238
  M1                5                13
  M1A               0                 1
  M1B               1                 2
  MX               29                90
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    49  66
  8P GAIN WILD-TYPE 199 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     49   66
  8P GAIN WILD-TYPE  199  148
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              49               199
  MALE                66               148
[1] 2 2
[1] FALSE
D15V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8P GAIN MUTATED                            4
  8P GAIN WILD-TYPE                          9
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8P GAIN MUTATED                                  27
  8P GAIN WILD-TYPE                                66
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                   72
  8P GAIN WILD-TYPE                                                222
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8P GAIN MUTATED                                            0
  8P GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  8P GAIN MUTATED                                               4
  8P GAIN WILD-TYPE                                            15
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  8P GAIN MUTATED                                0
  8P GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  8P GAIN MUTATED                                    0
  8P GAIN WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  8P GAIN MUTATED                              0                             6
  8P GAIN WILD-TYPE                            2                            13
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  8P GAIN MUTATED                                 0
  8P GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  8P GAIN MUTATED                                               1
  8P GAIN WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  8P GAIN MUTATED                              1
  8P GAIN WILD-TYPE                            6
D15V9, multiclass
                                                    clus
vv                                                   8P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              72
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    4
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    6
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   8P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               222
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     15
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     13
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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     7 108
  8P GAIN WILD-TYPE  14 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      7  108
  8P GAIN WILD-TYPE   14  333
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                7                14
  YES             108               333
[1] 2 2
[1] FALSE
D15V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    75   6   1   3
  8P GAIN WILD-TYPE 243   5   3  16
D15V12, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              75               243
  R1               6                 5
  R2               1                 3
  RX               3                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     2
  8P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           7    92
  8P GAIN WILD-TYPE                        19   270
D15V13, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      7                19
  WHITE                                         92               270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0  88
  8P GAIN WILD-TYPE   7 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   88
  8P GAIN WILD-TYPE    7  244
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              88               244
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   149  41
  8Q GAIN WILD-TYPE 172  41
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              190               213 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               41                41 
$`8Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4417 
        1523         1369         1126         1431          610          455 
TCGA-05-4424 TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-35-4122 
         913          761          457          151          670          225 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 
         264         1952         1492          864          354         1357 
TCGA-38-6178 TCGA-44-2656 TCGA-44-2668 TCGA-44-3918 TCGA-44-3919 TCGA-44-5644 
         448         1429          246         1036          190          863 
TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
         723          845          658         1942         1864         1978 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
         218          557         1970          882          535          719 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SU TCGA-49-4510 
          99          260          287          337           76          896 
TCGA-49-4512 TCGA-49-6761 TCGA-50-5051 TCGA-50-5066 TCGA-50-5072 TCGA-50-5931 
         157          354          455          944          246          267 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-53-7813 
        2370          567          764          686          255          424 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
         280          701         1479         1375           87          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6985 TCGA-55-7283 
          24         1239           25         1475         1233           35 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7907 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 
          95         1958           16            3           31           33 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
          26            4           47           15           33           46 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8507 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 
          44           23            8            9          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          15           48           66           42           29           48 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 
        1952           28            5          162         1216         1970 
TCGA-62-8402 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 
        1445         1246          910          628         1189         1126 
TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-69-7760 TCGA-69-7763 
          62          864           31          610          202          690 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K 
         414          230          184           89          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
          61         1600          711          131           40          164 
TCGA-73-4677 TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
          38          519         1970         1956         1965         1988 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 
        1944         1093         1202         1963         1221          215 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8660 
        1965         1972         1949          327         1952         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-7701 TCGA-86-7954 TCGA-86-8054 
        1964         1965         1972           11         1963          745 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8672 TCGA-86-8674 
          16           26           35           34           15          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6831 TCGA-91-6836 
          10           30           14          323          310          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-93-7347 TCGA-93-8067 
         372          842          492           36          297          186 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 TCGA-97-7547 TCGA-97-7553 TCGA-97-8172 
           2          568          476         1965         1332          182 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
          15          115          197          427          459           44 
TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N5 
         170          114          287          116            6          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        1946         1967         1951         1957         1951         1944 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1970         1970          142         1955 

$`8Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 TCGA-05-4415 
         607          426         1947          578         1958         1997 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         912          365          669          791          791          761 
TCGA-05-4433 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 
         730          882           30           62           14          182 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
        1962         1147         1073         1971          133         1324 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 
        1130         1163          722         1013          383          328 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 
         302          704          705         1938          444          592 
TCGA-44-7661 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS 
         366          385          486          466          351          415 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        1932         1081         1421          428          999          268 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 
        1700          445          369          890          522         2174 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 
        2146          785         1499          282         1091          653 
TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 
         883         1015          105         1986         1971         1178 
TCGA-55-6543 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
           2           67         1826         2151         1170           18 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 
         121            6            4           40           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
          34           24           54           19          197           21 
TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 
           5           21          100            6           43           66 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
         216           29           11           15          228            3 
TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF 
         146           49          106           33            1           47 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-64-1676 TCGA-64-1679 
        1289         2696         2067         2199         1728         1686 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
        1968         1959         1305         1559          866          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 
         427          385          174          141          422          186 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4662 
         165           70          382          100           77          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-7498 TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 
         800          467          621         1967         1973         1950 
TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 
        1963          760         1948         1957         1961          678 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 
        1940         1950         1934         1937         1944          881 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-6851 
         994         1949         1971         1981          824         1959 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 
         630          422         1968          591          508           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        1963           13           24          479          489          476 
TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 
         482         1955           19           45           18          455 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 
          39         1940           60           79          224           35 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-95-7039 
         197          174           44          218          127           34 
TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 
         377          477          121          964         1932          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
         181           22          107         1965           87          147 
TCGA-97-8547 TCGA-97-A4M7 TCGA-99-7458 TCGA-J2-8192 TCGA-J2-A4AE TCGA-J2-A4AG 
         148          271          392          154          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T7 
         578          435          285          622         1954         1954 
TCGA-MP-A4T9 TCGA-MP-A4TK TCGA-MP-A5C7 
        1980         1971         1490 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 1 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             2370              2696 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            437.5             482.0 
[1] "2.0 - 2370.0 (437.5)" "1.0 - 2696.0 (482.0)"
[1] "hr=" "1.4"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  8Q GAIN MUTATED         2       51       65        19        34         34
  8Q GAIN WILD-TYPE       2       62       66        24        35         33
                   vv
clus                STAGE IIIB STAGE IV
  8Q GAIN MUTATED            7       10
  8Q GAIN WILD-TYPE          4       13
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                51                62
  STAGE IB                65                66
  STAGE IIA               19                24
  STAGE IIB               34                35
  STAGE IIIA              34                33
  STAGE IIIB               7                 4
  STAGE IV                10                13
[1] 8 2
[1] 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    61 129  23   7
  8Q GAIN WILD-TYPE  82 130  17  11
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              61                82
  T2             129               130
  T3              23                17
  T4               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                 N0  N1 N2+N3
  8Q GAIN MUTATED   146  33    38
  8Q GAIN WILD-TYPE 149  52    34
D16V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                146               149
  N1                 33                52
  N2+N3              38                34
[1] 3 2
[1] 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 M1B  MX
  8Q GAIN MUTATED   150   8   0   2  60
  8Q GAIN WILD-TYPE 167  10   1   1  59
D16V6, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              150               167
  M1                8                10
  M1A               0                 1
  M1B               2                 1
  MX               60                59
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   115 107
  8Q GAIN WILD-TYPE 133 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    115  107
  8Q GAIN WILD-TYPE  133  107
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             115               133
  MALE               107               107
[1] 2 2
[1] FALSE
D16V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8Q GAIN MUTATED                            9
  8Q GAIN WILD-TYPE                          4
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8Q GAIN MUTATED                                  44
  8Q GAIN WILD-TYPE                                49
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                  148
  8Q GAIN WILD-TYPE                                                146
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8Q GAIN MUTATED                                            0
  8Q GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  8Q GAIN MUTATED                                               8
  8Q GAIN WILD-TYPE                                            11
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  8Q GAIN MUTATED                                1
  8Q GAIN WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  8Q GAIN MUTATED                                    0
  8Q GAIN WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  8Q GAIN MUTATED                              0                             9
  8Q GAIN WILD-TYPE                            2                            10
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  8Q GAIN MUTATED                                 1
  8Q GAIN WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  8Q GAIN MUTATED                                               2
  8Q GAIN WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  8Q GAIN MUTATED                              0
  8Q GAIN WILD-TYPE                            7
D16V9, multiclass
                                                    clus
vv                                                   8Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               44
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             148
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    8
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    9
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   8Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               146
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     11
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     10
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  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    11 211
  8Q GAIN WILD-TYPE  10 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     11  211
  8Q GAIN WILD-TYPE   10  230
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               11                10
  YES             211               230
[1] 2 2
[1] FALSE
D16V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   150   7   3   9
  8Q GAIN WILD-TYPE 168   4   1  10
D16V12, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             150               168
  R1               7                 4
  R2               3                 1
  RX               9                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     5
  8Q GAIN WILD-TYPE                                1     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          12   174
  8Q GAIN WILD-TYPE                        14   188
D16V13, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          5                 1
  BLACK OR AFRICAN AMERICAN                     12                14
  WHITE                                        174               188
[1] 4 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     3 156
  8Q GAIN WILD-TYPE   4 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  156
  8Q GAIN WILD-TYPE    4  176
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             156               176
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    32   5
  9P GAIN WILD-TYPE 289  77
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               37               366 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                5                77 
$`9P GAIN MUTATED`
TCGA-05-4390 TCGA-05-4410 TCGA-05-4427 TCGA-44-6147 TCGA-44-6774 TCGA-44-8119 
        1126         1958          791          845          658           99 
TCGA-44-A47F TCGA-50-5051 TCGA-50-6597 TCGA-55-6972 TCGA-55-7903 TCGA-55-7995 
         337          455         1015         1475           19            5 
TCGA-55-8301 TCGA-55-8514 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A4DF TCGA-64-5775 
          44          202           66           29           47           62 
TCGA-69-7973 TCGA-69-7979 TCGA-69-8253 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 
         230           89          100          214          711          800 
TCGA-73-7499 TCGA-78-7163 TCGA-78-8662 TCGA-80-5608 TCGA-86-7953 TCGA-86-8669 
         519         1950         1964         1972          591           34 
TCGA-91-6828 TCGA-95-7039 TCGA-95-7947 TCGA-97-7553 TCGA-97-7554 TCGA-L9-A444 
         323           34          477         1332          775            6 
TCGA-MP-A4TC 
        1944 

$`9P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 
        1523          607          426         1369         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
         578          610         1997          455          912          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         913          669          791          761          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         457          151          882          670           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          14          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1147         1492          864         1073          354         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
         448         1971          133         1324         1429          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1367          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1130         1163         1036          190          722         1013 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
         863          383          723          328          302          704 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         705         1938         1942         1864         1978          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         592          366          218          557         1970          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
         535          719          385          260          486          466 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         287          351          415           76         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        1700          445          369          890          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2174         2146          785          944         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         282          267         1091         2370          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         883          764          686          255          105         1986 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
        1971          424          280          701         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
        1375           87            2          993           24         1239 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
          25           67         1826         1233         2151         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
          18           35          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          54           16          197           21            3           31 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33           21          100            6           43           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           4           47           15           33           46           66 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
         216           23           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 
         228            9            3          146          536           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
          48           49          106           33           42           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 
        1952            1           28            5          162         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
        1289         1970         2696         1445         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        1246          910         1728          628         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1126         1968         1959         1305          864         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         866           31          610          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         174          141          422          202          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8254 
         414          165          184           70          382           77 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
         129           61         1600          912          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-75-7025 
          40          164           38          621         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1956         1965         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1093         1963         1202          760         1948         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1961         1963         1221          678          215         1940 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        1934         1937         1965         1972         1949         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
         327          881         1952          994         1949         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1981         1954         1965          824         1959           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         630          422         1968         1963          508          745 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
          10         1963           13           24          479          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         476          482           16         1955           19           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          35           45           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
          10           30           14           39         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
         310           79          417          372          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          35          492          197          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7567 
         218          297          127          186            2          568 
TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         377          476          121          964         1965         1932 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
         181           22          107          182         1965           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
         147           15          148          115          197          271 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         392          427          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         116          285          622          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1951         1954         1954         1957         1980         1951 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1970          142         1955         1971         1490 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                5                 1 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1972              2696 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            455.0             466.5 
[1] "5.0 - 1972.0 (455.0)" "1.0 - 2696.0 (466.5)"
[1] "hr=" "1"  
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  9P GAIN MUTATED         0       12       12         0         6          7
  9P GAIN WILD-TYPE       4      101      119        43        63         60
                   vv
clus                STAGE IIIB STAGE IV
  9P GAIN MUTATED            1        2
  9P GAIN WILD-TYPE         10       21
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                12               101
  STAGE IB                12               119
  STAGE IIA                0                43
  STAGE IIB                6                63
  STAGE IIIA               7                60
  STAGE IIIB               1                10
  STAGE IV                 2                21
[1] 8 2
[1] 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    18  17   4   1
  9P GAIN WILD-TYPE 125 242  36  17
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1              18               125
  T2              17               242
  T3               4                36
  T4               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                 N0  N1 N2+N3
  9P GAIN MUTATED    28   4     7
  9P GAIN WILD-TYPE 267  81    65
D17V5, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0                 28               267
  N1                  4                81
  N2+N3               7                65
[1] 3 2
[1] 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 M1B  MX
  9P GAIN MUTATED    28   1   0   1  10
  9P GAIN WILD-TYPE 289  17   1   2 109
D17V6, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               28               289
  M1                1                17
  M1A               0                 1
  M1B               1                 2
  MX               10               109
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    25  15
  9P GAIN WILD-TYPE 223 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     25   15
  9P GAIN WILD-TYPE  223  199
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              25               223
  MALE                15               199
[1] 2 2
[1] FALSE
D17V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9P GAIN MUTATED                            1
  9P GAIN WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9P GAIN MUTATED                                  11
  9P GAIN WILD-TYPE                                82
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                   23
  9P GAIN WILD-TYPE                                                271
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9P GAIN MUTATED                                            0
  9P GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  9P GAIN MUTATED                                               1
  9P GAIN WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  9P GAIN MUTATED                                0
  9P GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  9P GAIN MUTATED                                    0
  9P GAIN WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  9P GAIN MUTATED                              0                             3
  9P GAIN WILD-TYPE                            2                            16
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  9P GAIN MUTATED                                 1
  9P GAIN WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  9P GAIN MUTATED                                               0
  9P GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  9P GAIN MUTATED                              0
  9P GAIN WILD-TYPE                            7
D17V9, multiclass
                                                    clus
vv                                                   9P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              23
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   9P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               271
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     16
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  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     2  38
  9P GAIN WILD-TYPE  19 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   38
  9P GAIN WILD-TYPE   19  403
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                2                19
  YES              38               403
[1] 2 2
[1] FALSE
D17V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    27   0   1   2
  9P GAIN WILD-TYPE 291  11   3  17
D17V12, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              27               291
  R1               0                11
  R2               1                 3
  RX               2                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           3    30
  9P GAIN WILD-TYPE                        23   332
D17V13, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      3                23
  WHITE                                         30               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"
D17V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  32
  9P GAIN WILD-TYPE   7 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   32
  9P GAIN WILD-TYPE    7  300
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              32               300
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    23   4
  9Q GAIN WILD-TYPE 298  78
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               27               376 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                4                78 
$`9Q GAIN MUTATED`
TCGA-05-4390 TCGA-05-4427 TCGA-44-6147 TCGA-44-8119 TCGA-44-A47F TCGA-50-5051 
        1126          791          845           99          337          455 
TCGA-50-6597 TCGA-55-6972 TCGA-55-7995 TCGA-55-8091 TCGA-55-8301 TCGA-55-8620 
        1015         1475            5           43           44           66 
TCGA-55-A48Z TCGA-69-8253 TCGA-73-4666 TCGA-73-7499 TCGA-75-7031 TCGA-78-7160 
          29          100          800          519         1965          678 
TCGA-78-7163 TCGA-78-7542 TCGA-78-8662 TCGA-86-7953 TCGA-86-8669 TCGA-91-6836 
        1950         1952         1964          591           34          417 
TCGA-95-7947 TCGA-97-7553 TCGA-MP-A4TC 
         477         1332         1944 

$`9Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 
        1523          607          426         1369         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
         365          913          669          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         730          457          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1357          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1013          863          383          723          328          302 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         704          658          705         1938         1942         1864 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
        1978          444          592          366          218          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        1970          882          535          719          385          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         486          466          287          351          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        1932         1081         1421          428          999          268 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
         896          157         1700          445          369          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         522          354         2174         2146          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
        1499          246          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 
         653          567          883          764          686          255 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         105         1986         1971          424          280          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        1178         1479         1375           87            2          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
          24         1239           25           67         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        2151         1170           18           35          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40         1958           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
          34           24           54           19           16          197 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
          21            3           31           33           21          100 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
           6           26            4           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          46           66          216           23           29           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
           8           15          228            9            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
         202          536           15           48           49          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          33           42           48         1952            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           5           47          162         1216         1289         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        2696         1445         2067         2199         1246          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        1728          628         1189         1686         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1959           62         1305          864         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
          31          610          573          427          385          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
         141          422          202          186          690          414 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         165          230          184           70           89          382 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
          77          129          214           61         1600          711 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
         912          467          131           40          164           38 
TCGA-73-7498 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 
         621         1970         1967         1956         1973         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1950         1944         1093         1963         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 
        1948         1957         1961         1963         1221          215 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1940         1934         1937         1965         1972         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1944          327          881          994         1949         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1981         1954         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
          11          630          422         1968         1963          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
         745           10         1963           13           24          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
         489          476          482           16         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          26           35           45           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         405           10           30           14           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
        1940           60          310           79          372          842 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         224           35          492          197          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 
          44          218          297          127          186           34 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
           2          568          377          476          121          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
        1965         1932          775          181           22          107 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
         182         1965           87          147           15          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         115          197          271          392          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
          44          170          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         238          578          435          116            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         622          353         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1957         1980         1951         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5                 1 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1965              2696 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              591               456 
[1] "5.0 - 1965.0 (591.0)" "1.0 - 2696.0 (456.0)"
[1] "hr=" "1"  
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  9Q GAIN MUTATED         0        6       12         0         4          2
  9Q GAIN WILD-TYPE       4      107      119        43        65         65
                   vv
clus                STAGE IIIB STAGE IV
  9Q GAIN MUTATED            1        3
  9Q GAIN WILD-TYPE         10       20
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 6               107
  STAGE IB                12               119
  STAGE IIA                0                43
  STAGE IIB                4                65
  STAGE IIIA               2                65
  STAGE IIIB               1                10
  STAGE IV                 3                20
[1] 8 2
[1] 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    11  15   1   1
  9Q GAIN WILD-TYPE 132 244  39  17
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              11               132
  T2              15               244
  T3               1                39
  T4               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                 N0  N1 N2+N3
  9Q GAIN MUTATED    19   4     4
  9Q GAIN WILD-TYPE 276  81    68
D18V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0                 19               276
  N1                  4                81
  N2+N3               4                68
[1] 3 2
[1] 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 M1B  MX
  9Q GAIN MUTATED    19   2   0   1   6
  9Q GAIN WILD-TYPE 298  16   1   2 113
D18V6, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               19               298
  M1                2                16
  M1A               0                 1
  M1B               1                 2
  MX                6               113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    16  12
  9Q GAIN WILD-TYPE 232 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     16   12
  9Q GAIN WILD-TYPE  232  202
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              16               232
  MALE                12               202
[1] 2 2
[1] FALSE
D18V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9Q GAIN MUTATED                            0
  9Q GAIN WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9Q GAIN MUTATED                                   7
  9Q GAIN WILD-TYPE                                86
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                   19
  9Q GAIN WILD-TYPE                                                275
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9Q GAIN MUTATED                                            0
  9Q GAIN WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  9Q GAIN MUTATED                                               1
  9Q GAIN WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  9Q GAIN MUTATED                                0
  9Q GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  9Q GAIN MUTATED                                    0
  9Q GAIN WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  9Q GAIN MUTATED                              0                             1
  9Q GAIN WILD-TYPE                            2                            18
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  9Q GAIN MUTATED                                 0
  9Q GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  9Q GAIN MUTATED                                               0
  9Q GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  9Q GAIN MUTATED                              0
  9Q GAIN WILD-TYPE                            7
D18V9, multiclass
                                                    clus
vv                                                   9Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              19
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   9Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 86
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               275
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     18
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  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     1  27
  9Q GAIN WILD-TYPE  20 414
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   27
  9Q GAIN WILD-TYPE   20  414
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                20
  YES              27               414
[1] 2 2
[1] FALSE
D18V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    20   0   0   1
  9Q GAIN WILD-TYPE 298  11   4  18
D18V12, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              20               298
  R1               0                11
  R2               0                 4
  RX               1                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     0
  9Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           1    23
  9Q GAIN WILD-TYPE                        25   339
D18V13, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      1                25
  WHITE                                         23               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"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  21
  9Q GAIN WILD-TYPE   7 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   21
  9Q GAIN WILD-TYPE    7  311
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              21               311
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    75  17
  10P GAIN WILD-TYPE 246  65
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                92                311 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                17                 65 
$`10P GAIN MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1369         1126          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 
         912          365          913          761          761          457 
TCGA-05-5425 TCGA-35-4122 TCGA-38-4632 TCGA-44-3396 TCGA-44-3918 TCGA-44-6144 
         882          225         1357         1130         1036          723 
TCGA-44-6145 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-50-5049 
         328          535          719          385          260         2146 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5933 TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 
         455         1499         2370          686          255         1986 
TCGA-53-7813 TCGA-55-6642 TCGA-55-6972 TCGA-55-7283 TCGA-55-7910 TCGA-55-8092 
         424          993         1475           35          197           26 
TCGA-55-8302 TCGA-55-8511 TCGA-55-8615 TCGA-55-8620 TCGA-55-A491 TCGA-62-8398 
          23            9           15           66         1952         1970 
TCGA-64-1678 TCGA-69-7763 TCGA-69-7979 TCGA-71-6725 TCGA-73-4658 TCGA-73-4670 
        1189          690           89           61         1600          131 
TCGA-73-4675 TCGA-73-4677 TCGA-75-6214 TCGA-75-7027 TCGA-78-7149 TCGA-78-7154 
          40           38         1970         1956         1093         1948 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7539 TCGA-78-7542 
        1957         1221          678          215          327         1952 
TCGA-78-7633 TCGA-78-8662 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
         994         1964         1972           11          630          422 
TCGA-86-7955 TCGA-86-8358 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 
         508           19           15          455           10           30 
TCGA-91-6829 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 
        1940          417          492          186          568          377 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8179 TCGA-99-8025 TCGA-J2-8194 
        1332          775          181           15          427          114 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T7 
         116            6          285          622          353         1954 
TCGA-MP-A4T8 TCGA-MP-A4TE 
        1957         1970 

$`10P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          607          426         1947         1431          578 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 
         669          791          791          730          151          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          30           62           14          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
         448         1971          133         1324         1429          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1367          741         1280         1301           97          246 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1163          190          722         1013          863          383 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          845          704          658          705         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
        1942         1864         1978          444          592          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8119 TCGA-44-A479 
         218          557         1970          882           99          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         466          287          337          351          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        1932         1081         1421          428          999          268 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
         896          157         1700          445          369          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
         522          354         2174          785          944          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         282          267         1091          653          567          883 
TCGA-50-5944 TCGA-50-6597 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 
         764         1015          105         1971          280          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
        1178         1479         1375           87            2           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        1239           25           67         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1170           18          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          54           19           16           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33           21          100            6           43 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           4           47           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
         216           44           29           11            8           15 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
         228            3          146          202          536           48 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          49          106           33           42           29           48 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
           1           28            5           47          162         1216 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1289         2696         1445         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
         910         1728          628         1686         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1959           62         1305          864         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
          31          610          573          427          385          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
         141          422          202          186          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         230          184           70          382          100           77 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
         129          214          711          912          800          467 
TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 
         164          621          519         1967         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1988         1950         1944         1963         1202          760 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
        1961         1963         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 
        1965         1972         1949         1944          881         1949 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 
        1971         1981         1954         1965          824         1959 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
        1968          591         1963          745           10         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
          13           24          479          489          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
          16         1955           26           35           45           34 
TCGA-86-8671 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
          18          405           14           39          323           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
         310           79          372          842          224           35 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
         127           34            2          477          476          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
         964         1965         1932           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
        1965           87          147          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         271          392          459           44          170          154 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MP-A4SV 
         287          282          238          578          435         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1967         1951         1954         1980         1951         1944 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                  1 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              2370               2696 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               589                444 
[1] "6.0 - 2370.0 (589.0)" "1.0 - 2696.0 (444.0)"
[1] "hr=" "1.4"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  10P GAIN MUTATED         1       23       32         9        11         14
  10P GAIN WILD-TYPE       3       90       99        34        58         53
                    vv
clus                 STAGE IIIB STAGE IV
  10P GAIN MUTATED            4        7
  10P GAIN WILD-TYPE          7       16
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 23                 90
  STAGE IB                 32                 99
  STAGE IIA                 9                 34
  STAGE IIB                11                 58
  STAGE IIIA               14                 53
  STAGE IIIB                4                  7
  STAGE IV                  7                 16
[1] 8 2
[1] 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    22  63  11   5
  10P GAIN WILD-TYPE 121 196  29  13
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               22                121
  T2               63                196
  T3               11                 29
  T4                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                  N0  N1 N2+N3
  10P GAIN MUTATED    74  10    16
  10P GAIN WILD-TYPE 221  75    56
D19V5, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                  74                221
  N1                  10                 75
  N2+N3               16                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  10P GAIN MUTATED    71   6   0   1  23
  10P GAIN WILD-TYPE 246  12   1   2  96
D19V6, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                71                246
  M1                 6                 12
  M1A                0                  1
  M1B                1                  2
  MX                23                 96
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    40  61
  10P GAIN WILD-TYPE 208 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     40   61
  10P GAIN WILD-TYPE  208  153
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               40                208
  MALE                 61                153
[1] 2 2
[1] FALSE
D19V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10P GAIN MUTATED                            3
  10P GAIN WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10P GAIN MUTATED                                  24
  10P GAIN WILD-TYPE                                69
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                   62
  10P GAIN WILD-TYPE                                                232
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10P GAIN MUTATED                                            0
  10P GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  10P GAIN MUTATED                                               5
  10P GAIN WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  10P GAIN MUTATED                                0
  10P GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  10P GAIN MUTATED                                    1
  10P GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  10P GAIN MUTATED                              0                             6
  10P GAIN WILD-TYPE                            2                            13
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  10P GAIN MUTATED                                 0
  10P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  10P GAIN MUTATED                                               0
  10P GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  10P GAIN MUTATED                              0
  10P GAIN WILD-TYPE                            7
D19V9, multiclass
                                                    clus
vv                                                   10P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               62
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     6
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   10P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                232
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      13
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  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  99
  10P GAIN WILD-TYPE  19 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   99
  10P GAIN WILD-TYPE   19  342
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                 19
  YES               99                342
[1] 2 2
[1] FALSE
D19V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    67   3   0   8
  10P GAIN WILD-TYPE 251   8   4  11
D19V12, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               67                251
  R1                3                  8
  R2                0                  4
  RX                8                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     3
  10P GAIN WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           6    71
  10P GAIN WILD-TYPE                        20   291
D19V13, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                       6                 20
  WHITE                                          71                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"
D19V14, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2  64
  10P GAIN WILD-TYPE   5 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   64
  10P GAIN WILD-TYPE    5  268
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               64                268
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    51  14
  10Q GAIN WILD-TYPE 270  68
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                65                338 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                 68 
$`10Q GAIN MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4430 
        1369         1126         1997          455          365          761 
TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 TCGA-35-4122 TCGA-38-4632 TCGA-44-3918 
         761          457          882          225         1357         1036 
TCGA-44-6144 TCGA-44-6145 TCGA-44-7671 TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 
         723          328          535         2146          455         1499 
TCGA-50-5933 TCGA-50-5946 TCGA-53-7624 TCGA-55-6642 TCGA-55-6972 TCGA-55-7283 
        2370          686         1986          993         1475           35 
TCGA-55-8205 TCGA-55-8302 TCGA-55-8615 TCGA-55-A491 TCGA-62-8398 TCGA-69-7763 
          33           23           15         1952         1970          690 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-75-6214 
          61         1600          131           40           38         1970 
TCGA-75-7027 TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1956         1093         1948         1221          678          215 
TCGA-78-8662 TCGA-86-7701 TCGA-86-7713 TCGA-86-8279 TCGA-86-8358 TCGA-86-8672 
        1964           11          422          482           19           15 
TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-7771 TCGA-95-7567 TCGA-97-7553 
         455           10           30          492          568         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8179 TCGA-99-8025 TCGA-J2-8194 TCGA-MN-A4N4 
         775          181           15          427          114          622 
TCGA-MN-A4N5 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A5C7 
         353         1954         1957         1970         1490 

$`10Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          607          426         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
         610         1958          912          913          669          791 
TCGA-05-4427 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         791          730          151          670           30           62 
TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
          14          182          264         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
        1492          864         1073          354          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6146 
         190          722         1013          863          383          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
        1864         1978          444          592          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
         557         1970          882          719          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
         260          486          466          287          337          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         415           76         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         999          268          896          157         1700          445 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5055 
         369          890          522          354         2174          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
         944          246          282          267         1091          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         567          883          764         1015          255          105 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
        1971          424          280          701         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
        1375           87            2           24         1239           25 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
          67         1826         1233         2151         1170           18 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
          39           39           34           24           54           19 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          16          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33           21          100            6           43           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
           4           47           15           46           66          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
          44           29           11            8           15          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
           9            3          146          202          536           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
          49           66          106           33           42           29 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          48            1           28            5           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
        1216         1289         2696         1445         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        1246          910         1728          628         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1126         1968         1959           62         1305          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        1559          866           31          610          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         414          165          230          184           70           89 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 
         382          100           77          129          214          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 
         912          800          467          164          621          519 
TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1967         1965         1973         1988         1950         1944 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1963         1202          760         1957         1961         1963 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        1940         1950         1934         1937         1965         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1949         1944          327          881         1952          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 
        1949         1971         1981         1954         1965         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
         824         1959          630         1968          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
         508          745           10         1963           13           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 
         479          489          476           16         1955           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A4P7 
          35           45           34           18          405           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323         1940           60          310           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
         417          372          842          224           35          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         174           36           44          218          297          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
         186           34            2          377          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 
         121          964         1965         1932           22          107 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
         182         1965           87          147          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         197          271          392          459           44          170 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         154          287          282          238          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         116            6          285         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH 
        1954         1980         1951         1944         1970          142 
TCGA-MP-A4TI TCGA-MP-A4TK 
        1955         1971 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                  1 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              2370               2696 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             678.0              431.5 
[1] "10.0 - 2370.0 (678.0)" "1.0 - 2696.0 (431.5)" 
[1] "hr=" "1.3"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  10Q GAIN MUTATED         0       17       19         5         9         14
  10Q GAIN WILD-TYPE       4       96      112        38        60         53
                    vv
clus                 STAGE IIIB STAGE IV
  10Q GAIN MUTATED            3        6
  10Q GAIN WILD-TYPE          8       17
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                 17                 96
  STAGE IB                 19                112
  STAGE IIA                 5                 38
  STAGE IIB                 9                 60
  STAGE IIIA               14                 53
  STAGE IIIB                3                  8
  STAGE IV                  6                 17
[1] 8 2
[1] 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    16  44   9   4
  10Q GAIN WILD-TYPE 127 215  31  14
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               16                127
  T2               44                215
  T3                9                 31
  T4                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                  N0  N1 N2+N3
  10Q GAIN MUTATED    49   7    16
  10Q GAIN WILD-TYPE 246  78    56
D20V5, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                  49                246
  N1                   7                 78
  N2+N3               16                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  10Q GAIN MUTATED    53   6   0   0  14
  10Q GAIN WILD-TYPE 264  12   1   3 105
D20V6, multiclass
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                53                264
  M1                 6                 12
  M1A                0                  1
  M1B                0                  3
  MX                14                105
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    28  45
  10Q GAIN WILD-TYPE 220 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     28   45
  10Q GAIN WILD-TYPE  220  169
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               28                220
  MALE                 45                169
[1] 2 2
[1] FALSE
D20V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10Q GAIN MUTATED                            2
  10Q GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10Q GAIN MUTATED                                  19
  10Q GAIN WILD-TYPE                                74
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                   42
  10Q GAIN WILD-TYPE                                                252
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10Q GAIN MUTATED                                            0
  10Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  10Q GAIN MUTATED                                               3
  10Q GAIN WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  10Q GAIN MUTATED                                0
  10Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  10Q GAIN MUTATED                                    1
  10Q GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  10Q GAIN MUTATED                              0                             6
  10Q GAIN WILD-TYPE                            2                            13
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  10Q GAIN MUTATED                                 0
  10Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  10Q GAIN MUTATED                                               0
  10Q GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  10Q GAIN MUTATED                              0
  10Q GAIN WILD-TYPE                            7
D20V9, multiclass
                                                    clus
vv                                                   10Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               42
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     6
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   10Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                252
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      13
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  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  71
  10Q GAIN WILD-TYPE  19 370
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   71
  10Q GAIN WILD-TYPE   19  370
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 2                 19
  YES               71                370
[1] 2 2
[1] FALSE
D20V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    51   2   0   5
  10Q GAIN WILD-TYPE 267   9   4  14
D20V12, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               51                267
  R1                2                  9
  R2                0                  4
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     2
  10Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           3    53
  10Q GAIN WILD-TYPE                        23   309
D20V13, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       3                 23
  WHITE                                          53                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"
D20V14, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1  47
  10Q GAIN WILD-TYPE   6 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   47
  10Q GAIN WILD-TYPE    6  285
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               47                285
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    59  19
  11P GAIN WILD-TYPE 262  63
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                78                325 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                19                 63 
$`11P GAIN MUTATED`
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 TCGA-05-4432 TCGA-05-5420 
        1997          455          912          669          761          457 
TCGA-05-5423 TCGA-05-5429 TCGA-38-4628 TCGA-38-4629 TCGA-44-2659 TCGA-44-5645 
         151           30         1492          864         1367          383 
TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7661 TCGA-44-7669 TCGA-44-7670 
         705         1864         1978          366         1970          882 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU TCGA-49-4512 
          99          486          466          287           76          157 
TCGA-49-6743 TCGA-50-5933 TCGA-50-6597 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
         369         2370         1015          424          701         1178 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-7995 TCGA-55-8092 TCGA-55-8096 
           2           24           25            5           26           47 
TCGA-55-8205 TCGA-55-8514 TCGA-55-8620 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8399 
          33          202           66            5           47         2696 
TCGA-62-8402 TCGA-64-1677 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 
        1445          628         1968           62          864           31 
TCGA-67-3771 TCGA-67-6215 TCGA-69-7973 TCGA-69-7974 TCGA-71-6725 TCGA-73-4662 
         610          174          230          184           61          912 
TCGA-75-6214 TCGA-78-7163 TCGA-78-7167 TCGA-78-7542 TCGA-78-8655 TCGA-80-5608 
        1970         1950         1937         1952         1981         1972 
TCGA-86-6851 TCGA-86-7955 TCGA-86-8278 TCGA-86-8280 TCGA-86-A4P7 TCGA-91-6829 
        1959          508          476           16           14         1940 
TCGA-91-6840 TCGA-91-6848 TCGA-93-7348 TCGA-95-7043 TCGA-97-7554 TCGA-97-7937 
         372          224          127            2          775          181 
TCGA-97-8177 TCGA-99-8033 TCGA-L9-A443 TCGA-MN-A4N4 TCGA-MP-A4TA TCGA-MP-A4TC 
         147          170          116          622         1951         1944 

$`11P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4422 TCGA-05-4424 
        1431          578          610         1958          365          913 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 
         791          791          761          730          882          670 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
        1962         1147         1073          354         1357          448 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
        1971          133         1324         1429          400          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
        1036          190          722         1013          863          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
         328          302          845          704          658         1938 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 
        1942          444          592          218          557          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         719          385          260          337          351          415 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        1932         1081         1421          428          999          268 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
         896         1700          445          890          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        2174         2146          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 
         246          282          267         1091          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         883          764          686          255          105         1986 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
        1971          280         1479         1375           87          993 
TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        1239         1475           67         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1170           18           35          121            6            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
          95           40         1958           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          24           54           19           16          197           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
           3           31           33           21          100            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
          43            4           15           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          44           23           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 
         228            9            3          146          536           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
          48           49          106           33           42           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 
          48         1952            1           28          162         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1289         1970         2067         2199         1246          910 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 
        1728         1189         1686         1126         1959         1305 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 
        1559          866          573          427          385          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
          70           89          382          100           77          129 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
         214         1600          711          800          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 
          40          164           38          621          519         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1956         1965         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1093         1963         1202          760         1948         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1961         1963         1221          678          215         1940 
TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1934         1965         1972         1949         1944          327 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
         881          994         1949         1971         1954         1964 
TCGA-80-5607 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1965          824           11          630          422         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
         591         1963          745           10         1963           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 
          24          479          489          482         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          26           35           45           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 
         455          405           10           30           39          323 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6849 
          60          310           79          417          842           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          197          174           36           44          218 
TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         297          186           34          568          377          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         476          121          964         1965         1932         1332 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 
          22          107          182         1965           87           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
         148          115          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
         459           44          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 
         238          578          435            6          285          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
        1946         1967         1951         1954         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1980         1970         1970          142         1955         1971 
TCGA-MP-A5C7 
        1490 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                  1 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              2696               2199 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             461.5              467.0 
[1] "2.0 - 2696.0 (461.5)" "1.0 - 2199.0 (467.0)"
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  11P GAIN MUTATED         0       21       23         5        12         18
  11P GAIN WILD-TYPE       4       92      108        38        57         49
                    vv
clus                 STAGE IIIB STAGE IV
  11P GAIN MUTATED            4        5
  11P GAIN WILD-TYPE          7       18
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                 21                 92
  STAGE IB                 23                108
  STAGE IIA                 5                 38
  STAGE IIB                12                 57
  STAGE IIIA               18                 49
  STAGE IIIB                4                  7
  STAGE IV                  5                 18
[1] 8 2
[1] 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    28  49   4   5
  11P GAIN WILD-TYPE 115 210  36  13
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               28                115
  T2               49                210
  T3                4                 36
  T4                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                  N0  N1 N2+N3
  11P GAIN MUTATED    52  13    20
  11P GAIN WILD-TYPE 243  72    52
D21V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                  52                243
  N1                  13                 72
  N2+N3               20                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  11P GAIN MUTATED    56   4   0   1  26
  11P GAIN WILD-TYPE 261  14   1   2  93
D21V6, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                56                261
  M1                 4                 14
  M1A                0                  1
  M1B                1                  2
  MX                26                 93
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    56  32
  11P GAIN WILD-TYPE 192 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     56   32
  11P GAIN WILD-TYPE  192  182
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               56                192
  MALE                 32                182
[1] 2 2
[1] FALSE
D21V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11P GAIN MUTATED                            2
  11P GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11P GAIN MUTATED                                  16
  11P GAIN WILD-TYPE                                77
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                   59
  11P GAIN WILD-TYPE                                                235
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11P GAIN MUTATED                                            1
  11P GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  11P GAIN MUTATED                                               3
  11P GAIN WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  11P GAIN MUTATED                                1
  11P GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  11P GAIN MUTATED                                    1
  11P GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  11P GAIN MUTATED                              0                             4
  11P GAIN WILD-TYPE                            2                            15
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  11P GAIN MUTATED                                 1
  11P GAIN WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  11P GAIN MUTATED                                               0
  11P GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  11P GAIN MUTATED                              0
  11P GAIN WILD-TYPE                            7
D21V9, multiclass
                                                    clus
vv                                                   11P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                16
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               59
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   11P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                235
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      15
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  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     3  85
  11P GAIN WILD-TYPE  18 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3   85
  11P GAIN WILD-TYPE   18  356
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 3                 18
  YES               85                356
[1] 2 2
[1] FALSE
D21V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    60   2   1   3
  11P GAIN WILD-TYPE 258   9   3  16
D21V12, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               60                258
  R1                2                  9
  R2                1                  3
  RX                3                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     1
  11P GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           6    67
  11P GAIN WILD-TYPE                        20   295
D21V13, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       6                 20
  WHITE                                          67                295
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2  62
  11P GAIN WILD-TYPE   5 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   62
  11P GAIN WILD-TYPE    5  270
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               62                270
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    75  24
  11Q GAIN WILD-TYPE 246  58
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                99                304 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                24                 58 
$`11Q GAIN MUTATED`
TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 TCGA-05-4425 TCGA-05-4432 TCGA-05-5423 
        1958         1997          912          669          761          151 
TCGA-05-5429 TCGA-38-4628 TCGA-38-4629 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 
          30         1492          864         1429         1367         1280 
TCGA-44-5645 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
         383          658          705         1864         1978          592 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 
         366          218         1970          882          385           99 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU TCGA-49-4512 TCGA-49-6743 
         486          466          287           76          157          369 
TCGA-50-5933 TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
        2370         1015         1986          424          701         1178 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-7910 TCGA-55-7994 
        1375            2           24           25          197           31 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8506 TCGA-55-8510 TCGA-55-8514 
          26           47           33           11          228          202 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8399 
          48           66            5           47          162         2696 
TCGA-62-8402 TCGA-64-1677 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 
        1445          628         1968           62          864           31 
TCGA-67-3771 TCGA-67-6215 TCGA-69-7973 TCGA-69-7974 TCGA-69-A59K TCGA-71-6725 
         610          174          230          184          214           61 
TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-78-7154 TCGA-78-7155 
        1600          800          467          164         1948         1957 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
        1950         1937         1972         1981         1964         1972 
TCGA-86-6851 TCGA-86-7955 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
        1959          508          476          482           16           26 
TCGA-86-A4P7 TCGA-91-6829 TCGA-91-6840 TCGA-91-6848 TCGA-91-A4BC TCGA-93-7348 
          14         1940          372          224           44          127 
TCGA-95-7043 TCGA-97-7553 TCGA-97-7937 TCGA-97-8177 TCGA-99-8033 TCGA-L9-A443 
           2         1332          181          147          170          116 
TCGA-MN-A4N4 TCGA-MP-A4TA TCGA-MP-A4TC 
         622         1951         1944 

$`11Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
        1431          578          610          455          365          913 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 
         791          791          761          730          457          882 
TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         670           62           14          225          182          264 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1952         1962         1147         1073          354         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 
         448         1971          133         1324          400          741 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
         190          722         1013          863          723          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 
         302          845          704         1938         1942          444 
TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G 
         557          535          719          260          337          351 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
         415         1932         1081         1421          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
         268          896         1700          445          890          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         354         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
        1499          246          282          267         1091          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 
         567          883          764          686          255          105 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6969 
        1971          280         1479           87          993         1239 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        1475           67         1826         1233         2151         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
          18           35          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
          54           19           16           21            3            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
          33           21          100            6           43            4 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          15           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          29            8           15            9            3          146 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         536           15           49          106           33           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-62-8395 
          29           48         1952            1           28         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1289         1970         2067         2199         1246          910 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 
        1728         1189         1686         1126         1959         1305 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 
        1559          866          573          427          385          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
          70           89          382          100           77          129 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 
         711          912          131           40           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         519         1970         1967         1956         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1988         1950         1944         1093         1963         1202 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
         760         1961         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1940         1934         1965         1949         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 
         881         1952          994         1949         1971         1954 
TCGA-80-5607 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1965          824           11          630          422         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
         591         1963          745           10         1963           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 
          24          479          489         1955           19           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          45           34           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
          10           30           39          323           60          310 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
          79          417          842           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 
         174           36          218          297          186           34 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
         568          377          477          476          121          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1965         1932          775           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
        1965           87           15          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 
         271          392          427          459           44          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
           6          285          353         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1954         1957         1980         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                  1 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              2696               2199 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               467                458 
[1] "2.0 - 2696.0 (467.0)" "1.0 - 2199.0 (458.0)"
[1] "hr=" "1"  
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  11Q GAIN MUTATED         0       19       33         9        18         18
  11Q GAIN WILD-TYPE       4       94       98        34        51         49
                    vv
clus                 STAGE IIIB STAGE IV
  11Q GAIN MUTATED            4        7
  11Q GAIN WILD-TYPE          7       16
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                 19                 94
  STAGE IB                 33                 98
  STAGE IIA                 9                 34
  STAGE IIB                18                 51
  STAGE IIIA               18                 49
  STAGE IIIB                4                  7
  STAGE IV                  7                 16
[1] 8 2
[1] 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    28  64   9   5
  11Q GAIN WILD-TYPE 115 195  31  13
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               28                115
  T2               64                195
  T3                9                 31
  T4                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                  N0  N1 N2+N3
  11Q GAIN MUTATED    67  18    20
  11Q GAIN WILD-TYPE 228  67    52
D22V5, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                  67                228
  N1                  18                 67
  N2+N3               20                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  11Q GAIN MUTATED    67   6   0   1  33
  11Q GAIN WILD-TYPE 250  12   1   2  86
D22V6, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                67                250
  M1                 6                 12
  M1A                0                  1
  M1B                1                  2
  MX                33                 86
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    63  45
  11Q GAIN WILD-TYPE 185 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     63   45
  11Q GAIN WILD-TYPE  185  169
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               63                185
  MALE                 45                169
[1] 2 2
[1] FALSE
D22V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11Q GAIN MUTATED                            1
  11Q GAIN WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11Q GAIN MUTATED                                  17
  11Q GAIN WILD-TYPE                                76
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                   79
  11Q GAIN WILD-TYPE                                                215
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11Q GAIN MUTATED                                            1
  11Q GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  11Q GAIN MUTATED                                               4
  11Q GAIN WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  11Q GAIN MUTATED                                1
  11Q GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  11Q GAIN MUTATED                                    2
  11Q GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  11Q GAIN MUTATED                              0                             3
  11Q GAIN WILD-TYPE                            2                            16
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  11Q GAIN MUTATED                                 0
  11Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  11Q GAIN MUTATED                                               0
  11Q GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  11Q GAIN MUTATED                              0
  11Q GAIN WILD-TYPE                            7
D22V9, multiclass
                                                    clus
vv                                                   11Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               79
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   11Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                215
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      16
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  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     6 102
  11Q GAIN WILD-TYPE  15 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6  102
  11Q GAIN WILD-TYPE   15  339
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 6                 15
  YES              102                339
[1] 2 2
[1] FALSE
D22V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    71   2   1   4
  11Q GAIN WILD-TYPE 247   9   3  15
D22V12, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               71                247
  R1                2                  9
  R2                1                  3
  RX                4                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  1     2
  11Q GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           8    83
  11Q GAIN WILD-TYPE                        18   279
D22V13, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       8                 18
  WHITE                                          83                279
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3  79
  11Q GAIN WILD-TYPE   4 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   79
  11Q GAIN WILD-TYPE    4  253
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               79                253
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    86  22
  12P GAIN WILD-TYPE 235  60
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               108                295 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                22                 60 
$`12P GAIN MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4432 
        1369         1126         1997          455          912          761 
TCGA-05-5420 TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 TCGA-38-4632 TCGA-44-2668 
         457          670          225          264         1357          246 
TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
        1036         1013          863          592          557         1970 
TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A47A TCGA-49-6742 TCGA-50-5045 
         882          719           99          466          445         2174 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 TCGA-55-1594 TCGA-55-1595 
         246          267          567          764         1178         1479 
TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6980 TCGA-55-6985 
        1375          993           24           25           67         1233 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7576 TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 
        1170          121           40           39           24           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 
         197           21            5          100            4           47 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 TCGA-55-A490 
          23           29            8           15           15           48 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-62-A471 
          28            5           47         1970         1445         1246 
TCGA-64-1678 TCGA-64-1681 TCGA-64-5775 TCGA-67-3774 TCGA-69-7973 TCGA-69-7980 
        1189         1968           62          385          230          382 
TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-75-7027 TCGA-78-7145 
         214          800          131           40         1956         1973 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7154 TCGA-78-7159 TCGA-78-7167 TCGA-78-7220 
        1988         1944         1948         1221         1937         1965 
TCGA-78-8655 TCGA-86-6851 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8278 
        1981         1959          422          591         1963          476 
TCGA-86-8280 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 
          16           35           34           30          323         1940 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-93-8067 TCGA-95-7567 
         417          372          224           36          186          568 
TCGA-95-7944 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A443 
         377          115          271           44          170          116 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TI 
         285          622         1946         1954         1970         1955 

$`12P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          607          426         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
         610         1958          365          913          669          791 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
         791          761          730          151          882           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
          62           14          182         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
        1492          864         1073          354          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
        1280         1301           97         1130         1163          190 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         722          383          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         704          658          705         1938         1942         1864 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7671 TCGA-44-8117 
        1978          444          366          218          535          385 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         260          486          287          337          351          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
          76         1932         1081         1421          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
         268          896          157         1700          369          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         522          354         2146          455          785          944 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 
        1499          282         1091         2370          653          883 
TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         686         1015          255          105         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6969 
         424          280          701           87            2         1239 
TCGA-55-6972 TCGA-55-6983 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
        1475         1826         2151           18           35            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7815 
           4           95         1958           39           34           54 
TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
          19            3           31           33           21            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
          43           26           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
         216           44           11          228            9            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         146          202          536           48           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
         106           33           42           29         1952            1 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V 
         162         1216         1289         2696         2067         2199 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
         910         1728          628         1686         1126         1959 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1305          864         1559          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         573          427          174          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
         186          690          414          165          184           70 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 
          89          100           77          129           61         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         711          912          467          164           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7147 TCGA-78-7149 
         519         1970         1967         1965         1950         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1963         1202          760         1957         1961         1963 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
         678          215         1940         1950         1934         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1949         1944          327          881         1952          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1949         1971         1954         1964         1965         1972 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 
         824           11          630         1968          508          745 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
          10         1963           13           24          479          489 
TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 
         482         1955           19           26           45           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
          15          455          405           10           14           39 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 
          60          310           79          842           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         197          174           44          218          297          127 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
          34            2          477          476          121          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
        1965         1932         1332          775          181           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         107          182         1965           87          147           15 
TCGA-97-8547 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-J2-8192 
         148          197          392          427          459          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 
           6          353         1967         1951         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        1980         1951         1944         1970          142         1971 
TCGA-MP-A5C7 
        1490 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                  1 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              2174               2696 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             433.5              479.0 
[1] "4.0 - 2174.0 (433.5)" "1.0 - 2696.0 (479.0)"
[1] "hr=" "1"  
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  12P GAIN MUTATED         2       29       29        18        14         23
  12P GAIN WILD-TYPE       2       84      102        25        55         44
                    vv
clus                 STAGE IIIB STAGE IV
  12P GAIN MUTATED            2        9
  12P GAIN WILD-TYPE          9       14
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                 29                 84
  STAGE IB                 29                102
  STAGE IIA                18                 25
  STAGE IIB                14                 55
  STAGE IIIA               23                 44
  STAGE IIIB                2                  9
  STAGE IV                  9                 14
[1] 8 2
[1] 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    38  73  10   4
  12P GAIN WILD-TYPE 105 186  30  14
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               38                105
  T2               73                186
  T3               10                 30
  T4                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                  N0  N1 N2+N3
  12P GAIN MUTATED    77  23    23
  12P GAIN WILD-TYPE 218  62    49
D23V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                  77                218
  N1                  23                 62
  N2+N3               23                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  12P GAIN MUTATED    83   8   0   1  33
  12P GAIN WILD-TYPE 234  10   1   2  86
D23V6, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                83                234
  M1                 8                 10
  M1A                0                  1
  M1B                1                  2
  MX                33                 86
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    60  66
  12P GAIN WILD-TYPE 188 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     60   66
  12P GAIN WILD-TYPE  188  148
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               60                188
  MALE                 66                148
[1] 2 2
[1] FALSE
D23V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12P GAIN MUTATED                            2
  12P GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12P GAIN MUTATED                                  23
  12P GAIN WILD-TYPE                                70
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                   88
  12P GAIN WILD-TYPE                                                206
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12P GAIN MUTATED                                            0
  12P GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  12P GAIN MUTATED                                               6
  12P GAIN WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  12P GAIN MUTATED                                1
  12P GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  12P GAIN MUTATED                                    0
  12P GAIN WILD-TYPE                                  4
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  12P GAIN MUTATED                              0                             2
  12P GAIN WILD-TYPE                            2                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  12P GAIN MUTATED                                 0
  12P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  12P GAIN MUTATED                                               1
  12P GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  12P GAIN MUTATED                              3
  12P GAIN WILD-TYPE                            4
D23V9, multiclass
                                                    clus
vv                                                   12P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                23
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               88
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   12P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                206
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  4
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        4
[1] 12  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     5 121
  12P GAIN WILD-TYPE  16 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5  121
  12P GAIN WILD-TYPE   16  320
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 5                 16
  YES              121                320
[1] 2 2
[1] FALSE
D23V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    91   1   2   6
  12P GAIN WILD-TYPE 227  10   2  13
D23V12, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               91                227
  R1                1                 10
  R2                2                  2
  RX                6                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     3
  12P GAIN WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                           9    95
  12P GAIN WILD-TYPE                        17   267
D23V13, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                       9                 17
  WHITE                                          95                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"
D23V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1  88
  12P GAIN WILD-TYPE   6 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   88
  12P GAIN WILD-TYPE    6  244
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               88                244
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    84  18
  12Q GAIN WILD-TYPE 237  64
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               102                301 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                 64 
$`12Q GAIN MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4432 
        1369         1126         1997          455          912          761 
TCGA-05-5420 TCGA-05-5425 TCGA-35-4122 TCGA-35-5375 TCGA-44-2656 TCGA-44-3918 
         457          882          225          264         1429         1036 
TCGA-44-5644 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         863         1864          592          557         1970          882 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-6742 
         719           99          486          466          287          445 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 
        2174          455          246          267          567          764 
TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 
         424         1178         1479         1375          993           24 
TCGA-55-6971 TCGA-55-6987 TCGA-55-7284 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
          25         1170          121           39           24           54 
TCGA-55-7910 TCGA-55-7911 TCGA-55-8089 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
         197           21          100           23           29            8 
TCGA-55-8508 TCGA-55-8615 TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
          15           15           48         1952           28            5 
TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1678 
          47         1970         1445         2199         1246         1189 
TCGA-64-1681 TCGA-64-5779 TCGA-67-3774 TCGA-69-7973 TCGA-69-7980 TCGA-69-8255 
        1968          864          385          230          382          129 
TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-75-7027 TCGA-78-7145 
         214          800          131           40         1956         1973 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7167 TCGA-78-7220 TCGA-78-8655 TCGA-86-6851 
        1988         1944         1937         1965         1981         1959 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8278 TCGA-86-8358 
          11          422          591         1963          476           19 
TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6836 TCGA-91-6840 
          35           34           30          323          417          372 
TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 
         186          568          377          115          271           44 
TCGA-99-8033 TCGA-L9-A443 TCGA-MP-A4SV TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TI 
         170          116         1946         1954         1970         1955 

$`12Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          607          426         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
         610         1958          365          913          669          791 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
         791          761          730          151          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
          62           14          182         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
        1492          864         1073          354         1357          448 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        1971          133         1324          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
         190          722         1013          383          723          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          845          704          658          705         1938 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7671 
        1942         1978          444          366          218          535 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         385          260          337          351          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        1932         1081         1421          428          999          268 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         896          157         1700          369          890          522 
TCGA-49-6761 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
         354         2146          785          944         1499          282 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-5946 TCGA-50-6597 
        1091         2370          653          883          686         1015 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 
         255          105         1986         1971          280          701 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
          87            2         1239         1475           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 
        1233         2151           18           35            6            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 
          95           40         1958           39           34           19 
TCGA-55-7907 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          16            3           31            5           33           21 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
           6           43           26            4           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 
          33           46           66          216           44           11 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
          48           49           66          106           33           42 
TCGA-55-A48Z TCGA-55-A492 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
          29            1          162         1216         1289         2696 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 
        2067          910         1728          628         1686         1126 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        1959           62         1305         1559          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         610          573          427          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
         202          186          690          414          165          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 
          70           89          100           77           61         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         711          912          467          164           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7147 TCGA-78-7149 
         519         1970         1967         1965         1950         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1963         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1963         1221          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1934         1972         1949         1944          327          881 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
        1952          994         1949         1971         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 
        1965         1972          824          630         1968          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
         745           10         1963           13           24          479 
TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8668 
         489          482           16         1955           26           45 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
          18           15          455          405           10           14 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 
          39         1940           60          310           79          842 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         224           35          492          197          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 
          44          218          297          127           34            2 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         477          476          121          964         1965         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1332          775          181           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 
        1965           87          147           15          148          197 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         392          427          459          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 
         282          238          578          435            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 
         622          353         1967         1951         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        1980         1951         1944         1970          142         1971 
TCGA-MP-A5C7 
        1490 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                  1 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              2199               2696 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               456                476 
[1] "5.0 - 2199.0 (456.0)" "1.0 - 2696.0 (476.0)"
[1] "hr=" "1.5"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  12Q GAIN MUTATED         2       27       31        14        15         20
  12Q GAIN WILD-TYPE       2       86      100        29        54         47
                    vv
clus                 STAGE IIIB STAGE IV
  12Q GAIN MUTATED            3        8
  12Q GAIN WILD-TYPE          8       15
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                 27                 86
  STAGE IB                 31                100
  STAGE IIA                14                 29
  STAGE IIB                15                 54
  STAGE IIIA               20                 47
  STAGE IIIB                3                  8
  STAGE IV                  8                 15
[1] 8 2
[1] 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    35  71   9   4
  12Q GAIN WILD-TYPE 108 188  31  14
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               35                108
  T2               71                188
  T3                9                 31
  T4                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                  N0  N1 N2+N3
  12Q GAIN MUTATED    77  20    21
  12Q GAIN WILD-TYPE 218  65    51
D24V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                  77                218
  N1                  20                 65
  N2+N3               21                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  12Q GAIN MUTATED    80   8   0   0  31
  12Q GAIN WILD-TYPE 237  10   1   3  88
D24V6, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                80                237
  M1                 8                 10
  M1A                0                  1
  M1B                0                  3
  MX                31                 88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    59  61
  12Q GAIN WILD-TYPE 189 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     59   61
  12Q GAIN WILD-TYPE  189  153
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               59                189
  MALE                 61                153
[1] 2 2
[1] FALSE
D24V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12Q GAIN MUTATED                            3
  12Q GAIN WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12Q GAIN MUTATED                                  22
  12Q GAIN WILD-TYPE                                71
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                   83
  12Q GAIN WILD-TYPE                                                211
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12Q GAIN MUTATED                                            0
  12Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  12Q GAIN MUTATED                                               4
  12Q GAIN WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  12Q GAIN MUTATED                                1
  12Q GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  12Q GAIN MUTATED                                    0
  12Q GAIN WILD-TYPE                                  4
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  12Q GAIN MUTATED                              0                             2
  12Q GAIN WILD-TYPE                            2                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  12Q GAIN MUTATED                                 0
  12Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  12Q GAIN MUTATED                                               2
  12Q GAIN WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  12Q GAIN MUTATED                              3
  12Q GAIN WILD-TYPE                            4
D24V9, multiclass
                                                    clus
vv                                                   12Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               83
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   12Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                211
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  4
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        4
[1] 12  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     5 115
  12Q GAIN WILD-TYPE  16 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      5  115
  12Q GAIN WILD-TYPE   16  326
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 5                 16
  YES              115                326
[1] 2 2
[1] FALSE
D24V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    85   1   2   6
  12Q GAIN WILD-TYPE 233  10   2  13
D24V12, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               85                233
  R1                1                 10
  R2                2                  2
  RX                6                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     3
  12Q GAIN WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           7    89
  12Q GAIN WILD-TYPE                        19   273
D24V13, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                       7                 19
  WHITE                                          89                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"
D24V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  82
  12Q GAIN WILD-TYPE   5 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   82
  12Q GAIN WILD-TYPE    5  250
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               82                250
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    28  10
  13Q GAIN WILD-TYPE 293  72
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                38                365 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                 72 
$`13Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-5428 TCGA-38-4631 TCGA-44-2655 TCGA-44-2659 
        1523          607          670          354         1324         1367 
TCGA-44-7660 TCGA-44-7671 TCGA-49-6742 TCGA-53-7624 TCGA-53-7626 TCGA-55-7281 
         592          535          445         1986         1971           18 
TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 TCGA-55-8089 TCGA-55-8205 TCGA-55-8620 
          39           16          197          100           33           66 
TCGA-55-A492 TCGA-62-8402 TCGA-64-1678 TCGA-64-1680 TCGA-67-3771 TCGA-67-3772 
           1         1445         1189         1126          610          573 
TCGA-67-6215 TCGA-69-8253 TCGA-73-4677 TCGA-75-6214 TCGA-75-7027 TCGA-78-7149 
         174          100           38         1970         1956         1093 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-86-8074 TCGA-86-8672 TCGA-97-7547 
        1937         1965         1944           24           15         1965 
TCGA-MP-A4SW TCGA-MP-A4T7 
        1967         1954 

$`13Q GAIN WILD-TYPE`
TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         426         1369         1126         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
         610         1958         1997          455          912          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         913          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
         730          457          151          882           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          14          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
        1147         1492          864         1073         1357          448 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
        1971          133         1429          400          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
         190          722         1013          863          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 
        1938         1942         1864         1978          444          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
         218          557         1970          882          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
          99          260          486          466          287          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         351          415           76         1932         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896          157         1700 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
         369          890          522          354         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         267         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 
         764          686         1015          255          105          424 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         280          701         1178         1479         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
           2          993           24         1239           25         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 
          67         1826         1233         2151         1170           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40         1958 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
          39           34           24           54           19           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
           3           31            5           33           21            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
          43           26            4           47           15           46 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          66          216           44           23           29           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
           8           15          228            9            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
         202          536           15           48           49          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
          33           42           29           48         1952           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           5           47          162         1216         1289         1970 
TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
        2696         2067         2199         1246          910         1728 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
         628         1686         1968         1959           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 
         864         1559          866           31          427          385 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
         141          422          202          186          690          414 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         165          230          184           70           89          382 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
          77          129          214           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         912          800          467          131           40          164 
TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
         621          519         1967         1965         1973         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1950         1944         1963         1202          760         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1957         1961         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
        1940         1950         1934         1972         1949          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881         1952          994         1949         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
          11          630          422         1968          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
         508          745           10         1963           13          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
         489          476          482           16         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
          26           35           45           34           18          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         405           10           30           14           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
        1940           60          310           79          417          372 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         842          224           35          492          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
          36           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
          34            2          568          377          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         121          964         1932         1332          775          181 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
          22          107          182         1965           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
          15          148          115          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         427          459           44          170          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         287          282          238          578          435          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 
           6          285          622          353         1946         1951 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                  2 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              1986               2696 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             608.5              455.0 
[1] "1.0 - 1986.0 (608.5)" "2.0 - 2696.0 (455.0)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  13Q GAIN MUTATED         0        8       11         7         6          3
  13Q GAIN WILD-TYPE       4      105      120        36        63         64
                    vv
clus                 STAGE IIIB STAGE IV
  13Q GAIN MUTATED            1        6
  13Q GAIN WILD-TYPE         10       17
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  8                105
  STAGE IB                 11                120
  STAGE IIA                 7                 36
  STAGE IIB                 6                 63
  STAGE IIIA                3                 64
  STAGE IIIB                1                 10
  STAGE IV                  6                 17
[1] 8 2
[1] 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    14  26   1   1
  13Q GAIN WILD-TYPE 129 233  39  17
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               14                129
  T2               26                233
  T3                1                 39
  T4                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                  N0  N1 N2+N3
  13Q GAIN MUTATED    28  10     4
  13Q GAIN WILD-TYPE 267  75    68
D25V5, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                  28                267
  N1                  10                 75
  N2+N3                4                 68
[1] 3 2
[1] 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 M1B  MX
  13Q GAIN MUTATED    30   5   0   1   6
  13Q GAIN WILD-TYPE 287  13   1   2 113
D25V6, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                30                287
  M1                 5                 13
  M1A                0                  1
  M1B                1                  2
  MX                 6                113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    23  19
  13Q GAIN WILD-TYPE 225 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     23   19
  13Q GAIN WILD-TYPE  225  195
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               23                225
  MALE                 19                195
[1] 2 2
[1] FALSE
D25V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  13Q GAIN MUTATED                            0
  13Q GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  13Q GAIN MUTATED                                   9
  13Q GAIN WILD-TYPE                                84
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                   29
  13Q GAIN WILD-TYPE                                                265
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  13Q GAIN MUTATED                                            0
  13Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  13Q GAIN MUTATED                                               1
  13Q GAIN WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  13Q GAIN MUTATED                                0
  13Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  13Q GAIN MUTATED                                    0
  13Q GAIN WILD-TYPE                                  4
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  13Q GAIN MUTATED                              0                             2
  13Q GAIN WILD-TYPE                            2                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  13Q GAIN MUTATED                                 0
  13Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  13Q GAIN MUTATED                                               0
  13Q GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  13Q GAIN MUTATED                              1
  13Q GAIN WILD-TYPE                            6
D25V9, multiclass
                                                    clus
vv                                                   13Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               29
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   13Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                265
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  4
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     2  40
  13Q GAIN WILD-TYPE  19 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2   40
  13Q GAIN WILD-TYPE   19  401
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 2                 19
  YES               40                401
[1] 2 2
[1] FALSE
D25V11, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED    36   0   0   0
  13Q GAIN WILD-TYPE 282  11   4  19
D25V12, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               36                282
  R1                0                 11
  R2                0                  4
  RX                0                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     0
  13Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           4    31
  13Q GAIN WILD-TYPE                        22   331
D25V13, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       4                 22
  WHITE                                          31                331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1  27
  13Q GAIN WILD-TYPE   6 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   27
  13Q GAIN WILD-TYPE    6  305
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               27                305
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    76  19
  14Q GAIN WILD-TYPE 245  63
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                95                308 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                19                 63 
$`14Q GAIN MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4424 TCGA-35-4123 
        1369         1126         1997          455          913          182 
TCGA-35-5375 TCGA-38-4627 TCGA-38-4629 TCGA-44-2659 TCGA-44-2668 TCGA-44-6147 
         264         1147          864         1367          246          845 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-8119 
        1864         1978          592          218          557           99 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU TCGA-49-4486 TCGA-49-4512 
         486          466          287           76         1932          157 
TCGA-50-5941 TCGA-50-5946 TCGA-50-7109 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
         567          686          255          280           87            2 
TCGA-55-6971 TCGA-55-6983 TCGA-55-7724 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
          25         1826         1958           54           16          197 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8091 TCGA-55-8096 TCGA-55-8206 TCGA-55-8302 
           5           33           43           47           46           23 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8614 TCGA-55-A490 TCGA-55-A4DG 
          11            8          228          536           48          162 
TCGA-64-1677 TCGA-64-5774 TCGA-64-5775 TCGA-67-3770 TCGA-67-3771 TCGA-69-7763 
         628         1959           62           31          610          690 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         230          184           89           61         1600          711 
TCGA-73-4666 TCGA-73-4677 TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 
         800           38          519         1967         1965         1973 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-80-5608 
        1944         1093         1221          215         1937         1972 
TCGA-83-5908 TCGA-86-7955 TCGA-86-8074 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 
         824          508           24          476           16           19 
TCGA-86-8585 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
          35          323           79          417          372          842 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-93-8067 TCGA-97-7546 TCGA-97-8179 
         197          174           36          186          964           15 
TCGA-J2-8192 TCGA-L9-A443 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
         154          116         1980         1970         1970 

$`14Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          607          426         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
         610         1958          912          365          669          791 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
         791          761          761          730          457          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         882          670           30           62           14          225 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1952         1962         1492         1073          354         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
         448         1971          133         1324         1429          400 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
         741         1280         1301           97         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1036          190          722         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         723          328          302          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7669 TCGA-44-7670 
        1938         1942          444          366         1970          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G 
         535          719          385          260          337          351 
TCGA-44-A4SS TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
         415         1081         1421          428          999          268 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         896         1700          445          369          890          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         354         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
        1499          246          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 
         653          883          764         1015          105         1986 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
        1971          424          701         1178         1479         1375 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 
         993           24         1239         1475           67         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        2151         1170           18           35          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
           4           95           40           39           39           34 
TCGA-55-7728 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8087 
          24           19           21            3           31           21 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 
         100            6           26            4           15           33 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8508 TCGA-55-8511 
          66          216           44           29           15            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
           3          146          202           15           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 
          66          106           33           42           29         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 
           1           28            5           47         1216         1289 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1970         2696         1445         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
         910         1728         1189         1686         1126         1968 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
        1305          864         1559          866          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         414          165           70          382          100           77 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
         129          214          912          467          131           40 
TCGA-73-4676 TCGA-73-7498 TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7147 
         164          621         1970         1956         1988         1950 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1963         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
        1963          678         1940         1950         1934         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1972         1949         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         994         1949         1971         1981         1954         1964 
TCGA-80-5607 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1965         1959           11          630          422         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
         591         1963          745           10         1963           13 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8281 TCGA-86-8359 TCGA-86-8668 
         479          489          482         1955           26           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          34           18           15          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          30           14           39         1940           60          310 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         224           35          492           44          218          297 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         127           34            2          568          377          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         476          121         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
         181           22          107          182         1965           87 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
         147          148          115          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD 
         427          459           44          170          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 
         282          238          578          435            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         622          353         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI 
        1954         1957         1951         1944          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                  1 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1997               2696 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             323.0              480.5 
[1] "2.0 - 1997.0 (323.0)" "1.0 - 2696.0 (480.5)"
[1] "hr=" "1.2"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  14Q GAIN MUTATED         1       30       34        12        14         13
  14Q GAIN WILD-TYPE       3       83       97        31        55         54
                    vv
clus                 STAGE IIIB STAGE IV
  14Q GAIN MUTATED            3        5
  14Q GAIN WILD-TYPE          8       18
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 30                 83
  STAGE IB                 34                 97
  STAGE IIA                12                 31
  STAGE IIB                14                 55
  STAGE IIIA               13                 54
  STAGE IIIB                3                  8
  STAGE IV                  5                 18
[1] 8 2
[1] 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    35  63   9   5
  14Q GAIN WILD-TYPE 108 196  31  13
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               35                108
  T2               63                196
  T3                9                 31
  T4                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                  N0  N1 N2+N3
  14Q GAIN MUTATED    78  16    14
  14Q GAIN WILD-TYPE 217  69    58
D26V5, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                  78                217
  N1                  16                 69
  N2+N3               14                 58
[1] 3 2
[1] 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 M1B  MX
  14Q GAIN MUTATED    63   5   0   0  44
  14Q GAIN WILD-TYPE 254  13   1   3  75
D26V6, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                63                254
  M1                 5                 13
  M1A                0                  1
  M1B                0                  3
  MX                44                 75
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    64  48
  14Q GAIN WILD-TYPE 184 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     64   48
  14Q GAIN WILD-TYPE  184  166
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               64                184
  MALE                 48                166
[1] 2 2
[1] FALSE
D26V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  14Q GAIN MUTATED                            4
  14Q GAIN WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  14Q GAIN MUTATED                                  17
  14Q GAIN WILD-TYPE                                76
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                   80
  14Q GAIN WILD-TYPE                                                214
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  14Q GAIN MUTATED                                            1
  14Q GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  14Q GAIN MUTATED                                               2
  14Q GAIN WILD-TYPE                                            17
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  14Q GAIN MUTATED                                0
  14Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  14Q GAIN MUTATED                                    1
  14Q GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  14Q GAIN MUTATED                              0                             4
  14Q GAIN WILD-TYPE                            2                            15
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  14Q GAIN MUTATED                                 0
  14Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  14Q GAIN MUTATED                                               2
  14Q GAIN WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  14Q GAIN MUTATED                              1
  14Q GAIN WILD-TYPE                            6
D26V9, multiclass
                                                    clus
vv                                                   14Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               80
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   14Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                214
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      17
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      15
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     2 110
  14Q GAIN WILD-TYPE  19 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2  110
  14Q GAIN WILD-TYPE   19  331
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 2                 19
  YES              110                331
[1] 2 2
[1] FALSE
D26V11, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    72   5   1   6
  14Q GAIN WILD-TYPE 246   6   3  13
D26V12, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               72                246
  R1                5                  6
  R2                1                  3
  RX                6                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     2
  14Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           5    92
  14Q GAIN WILD-TYPE                        21   270
D26V13, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       5                 21
  WHITE                                          92                270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  83
  14Q GAIN WILD-TYPE   6 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   83
  14Q GAIN WILD-TYPE    6  249
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               83                249
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    20  12
  15Q GAIN WILD-TYPE 301  70
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                32                371 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                12                 70 
$`15Q GAIN MUTATED`
TCGA-05-4403 TCGA-05-4415 TCGA-05-4420 TCGA-05-5420 TCGA-44-2661 TCGA-44-5645 
         578         1997          912          457          741          383 
TCGA-49-4506 TCGA-49-6742 TCGA-50-5072 TCGA-50-5944 TCGA-55-1594 TCGA-55-7284 
         999          445          246          764         1178          121 
TCGA-55-8207 TCGA-55-8505 TCGA-62-8398 TCGA-62-8402 TCGA-64-1678 TCGA-69-7980 
          66           29         1970         1445         1189          382 
TCGA-71-6725 TCGA-73-4670 TCGA-78-7148 TCGA-78-7149 TCGA-78-7154 TCGA-78-7220 
          61          131         1944         1093         1948         1965 
TCGA-78-7540 TCGA-78-8662 TCGA-86-8055 TCGA-95-7944 TCGA-97-7553 TCGA-97-8174 
         881         1964           10          377         1332         1965 
TCGA-97-8552 TCGA-MP-A4T7 
         115         1954 

$`15Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
        1431          610         1958          455          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         669          791          791          761          761          730 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         151          882          670           30           62           14 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
         225          182          264         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
        1492          864         1073          354         1357          448 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
        1971          133         1324         1429          400         1367 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
        1036          190          722         1013          863          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
        1938         1942         1864         1978          444          592 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         366          218          557         1970          882          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
         719          385           99          260          486          466 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         287          337          351          415           76         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1081         1421          428          268          896          157 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
        1700          369          890          522          354         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
        2146          455          785          944         1499          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         267         1091         2370          653          567          883 
TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         686         1015          255          105         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         424          280          701         1479         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
           2          993           24         1239           25         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
          67         1826         1233         2151         1170           18 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
          35            6            4           95           40         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
          39           39           34           24           54           19 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          16          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33           21          100            6           43           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8299 
           4           47           15           33           46          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
          44           23           11            8           15          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
           9            3          146          202          536           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
          48           49           66          106           33           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          29           48         1952            1           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U 
          47          162         1216         1289         2696         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
        2199         1246          910         1728          628         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1126         1968         1959           62         1305          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        1559          866           31          610          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         690          414          165          230          184           70 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 
          89          100           77          129          214         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
         711          912          800          467           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
          38          621          519         1970         1967         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 
        1965         1973         1988         1950         1963         1202 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
         760         1957         1961         1963         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 
         215         1940         1950         1934         1937         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1949         1944          327         1952          994         1949 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
        1971         1981         1954         1965         1972          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        1959           11          630          422         1968          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
        1963          508          745         1963           13           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
         479          489          476          482           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          19           26           35           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          15          455          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323         1940           60          310           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
         417          372          842          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 
         127          186           34            2          568          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 
         476          121          964         1965         1932          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 
         181           22          107          182           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
          15          148          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         282          238          578          435          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         285          622          353         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                  1 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1997               2696 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             822.5              455.0 
[1] "10.0 - 1997.0 (822.5)" "1.0 - 2696.0 (455.0)" 
[1] "hr=" "1.6"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  15Q GAIN MUTATED         2        5        6         3         4         10
  15Q GAIN WILD-TYPE       2      108      125        40        65         57
                    vv
clus                 STAGE IIIB STAGE IV
  15Q GAIN MUTATED            2        2
  15Q GAIN WILD-TYPE          9       21
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                  5                108
  STAGE IB                  6                125
  STAGE IIA                 3                 40
  STAGE IIB                 4                 65
  STAGE IIIA               10                 57
  STAGE IIIB                2                  9
  STAGE IV                  2                 21
[1] 8 2
[1] 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     8  21   3   2
  15Q GAIN WILD-TYPE 135 238  37  16
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                8                135
  T2               21                238
  T3                3                 37
  T4                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                  N0  N1 N2+N3
  15Q GAIN MUTATED    18   4    11
  15Q GAIN WILD-TYPE 277  81    61
D27V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                  18                277
  N1                   4                 81
  N2+N3               11                 61
[1] 3 2
[1] 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 M1B  MX
  15Q GAIN MUTATED    26   2   0   0   5
  15Q GAIN WILD-TYPE 291  16   1   3 114
D27V6, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                26                291
  M1                 2                 16
  M1A                0                  1
  M1B                0                  3
  MX                 5                114
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    15  19
  15Q GAIN WILD-TYPE 233 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     15   19
  15Q GAIN WILD-TYPE  233  195
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               15                233
  MALE                 19                195
[1] 2 2
[1] FALSE
D27V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  15Q GAIN MUTATED                            2
  15Q GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  15Q GAIN MUTATED                                   9
  15Q GAIN WILD-TYPE                                84
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                   15
  15Q GAIN WILD-TYPE                                                279
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  15Q GAIN MUTATED                                            1
  15Q GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  15Q GAIN MUTATED                                               3
  15Q GAIN WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  15Q GAIN MUTATED                                0
  15Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  15Q GAIN MUTATED                                    0
  15Q GAIN WILD-TYPE                                  4
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  15Q GAIN MUTATED                              0                             2
  15Q GAIN WILD-TYPE                            2                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  15Q GAIN MUTATED                                 0
  15Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  15Q GAIN MUTATED                                               0
  15Q GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  15Q GAIN MUTATED                              2
  15Q GAIN WILD-TYPE                            5
D27V9, multiclass
                                                    clus
vv                                                   15Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               15
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   15Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  4
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        5
[1] 12  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  32
  15Q GAIN WILD-TYPE  19 409
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2   32
  15Q GAIN WILD-TYPE   19  409
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 2                 19
  YES               32                409
[1] 2 2
[1] FALSE
D27V11, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    25   1   0   1
  15Q GAIN WILD-TYPE 293  10   4  18
D27V12, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               25                293
  R1                1                 10
  R2                0                  4
  RX                1                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     1
  15Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           1    25
  15Q GAIN WILD-TYPE                        25   337
D27V13, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       1                 25
  WHITE                                          25                337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  21
  15Q GAIN WILD-TYPE   7 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   21
  15Q GAIN WILD-TYPE    7  311
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               21                311
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    85  21
  16P GAIN WILD-TYPE 236  61
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               106                297 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                21                 61 
$`16P GAIN MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-5423 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        1523         1126          151         1147         1492          864 
TCGA-38-4631 TCGA-38-6178 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-3919 
         354          448         1367         1280         1301          190 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6147 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 
         863          383          845          705         1864         1978 
TCGA-44-7662 TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU TCGA-49-4505 
         218         1970          466          287           76          428 
TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-50-5933 TCGA-50-5935 TCGA-50-6597 
         268          157          890         2370          653         1015 
TCGA-50-8460 TCGA-55-1592 TCGA-55-6712 TCGA-55-6980 TCGA-55-7281 TCGA-55-7284 
         105          701           24           67           18          121 
TCGA-55-7573 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8091 
           4           39           16          197            5           43 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8512 TCGA-55-8615 
          26           47           15           46            3           15 
TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8398 TCGA-64-1676 
          66           48           28          162         1970         1728 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-67-3772 TCGA-67-6215 TCGA-67-6217 
        1686         1126         1968          573          174          422 
TCGA-69-7760 TCGA-69-7764 TCGA-69-7978 TCGA-69-7980 TCGA-71-6725 TCGA-73-4658 
         202          414           70          382           61         1600 
TCGA-73-4668 TCGA-73-4675 TCGA-75-7025 TCGA-78-7152 TCGA-78-7154 TCGA-78-7156 
         467           40         1967         1202         1948         1961 
TCGA-78-7163 TCGA-78-7542 TCGA-78-8640 TCGA-86-7701 TCGA-86-7713 TCGA-86-7955 
        1950         1952         1949           11          422          508 
TCGA-86-8055 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
          10          479          476          482           16           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6840 TCGA-91-8496 
          35           45           10           30          372          197 
TCGA-91-8497 TCGA-93-7348 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
         174          127          477          121          964         1965 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 
         147           15          115          271          427          170 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-MN-A4N4 TCGA-MP-A4SW 
         287          238          622         1967 

$`16P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         607          426         1369         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
         610         1958         1997          455          912          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         913          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         730          457          882          670           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          14          225          182          264         1952         1962 
TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1073         1357         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
         400          741           97          246         1130         1163 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1036          722         1013          723          328          302 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 
         704          658         1938         1942          444          592 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         366          557          882          535          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
          99          260          486          337          351          415 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 
        1932         1081         1421          999          896         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
         445          369          522          354         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
         267         1091          567          883          764          686 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
         255         1986         1971          424          280         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 
        1479         1375           87            2          993         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
          25         1475         1826         1233         2151         1170 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
          35            6           95           40         1958           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 
          34           24           54           19           21            3 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8094 
          31           33           21          100            6            4 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          33           66          216           44           23           29 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 
          11            8           15          228            9          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
         202          536           48           49          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF 
          42           29         1952            1            5           47 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
        1216         1289         2696         1445         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 
        1246          910          628         1189         1959           62 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1305          864         1559          866           31          610 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 
         427          385          141          186          690          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
         230          184           89          100           77          129 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 
         214          711          912          800          131          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 
          38          621          519         1970         1956         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1973         1988         1950         1944         1093         1963 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
         760         1957         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1940         1934         1937         1965         1972         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
        1944          327          881          994         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 
         630         1968          591         1963          745         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8281 TCGA-86-8358 TCGA-86-8669 
          13           24          489         1955           19           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 
          18           15          455          405           14           39 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
         323         1940           60          310           79          417 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC 
         842          224           35          492           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
         218          297          186           34            2          568 
TCGA-95-7944 TCGA-95-7948 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         377          476         1932         1332          775          181 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8547 
          22          107          182         1965           87          148 
TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 
         197          392          459           44          154          114 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         282          578          435          116            6          285 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
         353         1946         1951         1954         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1980         1951         1944         1970         1970          142 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                  1 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              2370               2696 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               363                567 
[1] "3.0 - 2370.0 (363.0)" "1.0 - 2696.0 (567.0)"
[1] "hr=" "1.4"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  16P GAIN MUTATED         2       32       31        14        15         15
  16P GAIN WILD-TYPE       2       81      100        29        54         52
                    vv
clus                 STAGE IIIB STAGE IV
  16P GAIN MUTATED            2        7
  16P GAIN WILD-TYPE          9       16
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                 32                 81
  STAGE IB                 31                100
  STAGE IIA                14                 29
  STAGE IIB                15                 54
  STAGE IIIA               15                 52
  STAGE IIIB                2                  9
  STAGE IV                  7                 16
[1] 8 2
[1] 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    41  61  12   3
  16P GAIN WILD-TYPE 102 198  28  15
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               41                102
  T2               61                198
  T3               12                 28
  T4                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                  N0  N1 N2+N3
  16P GAIN MUTATED    72  25    17
  16P GAIN WILD-TYPE 223  60    55
D28V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                  72                223
  N1                  25                 60
  N2+N3               17                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  16P GAIN MUTATED    77   5   0   2  31
  16P GAIN WILD-TYPE 240  13   1   1  88
D28V6, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                77                240
  M1                 5                 13
  M1A                0                  1
  M1B                2                  1
  MX                31                 88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    62  56
  16P GAIN WILD-TYPE 186 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     62   56
  16P GAIN WILD-TYPE  186  158
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               62                186
  MALE                 56                158
[1] 2 2
[1] FALSE
D28V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16P GAIN MUTATED                            3
  16P GAIN WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16P GAIN MUTATED                                  14
  16P GAIN WILD-TYPE                                79
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                   86
  16P GAIN WILD-TYPE                                                208
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16P GAIN MUTATED                                            1
  16P GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  16P GAIN MUTATED                                               6
  16P GAIN WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  16P GAIN MUTATED                                0
  16P GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  16P GAIN MUTATED                                    1
  16P GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  16P GAIN MUTATED                              0                             6
  16P GAIN WILD-TYPE                            2                            13
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  16P GAIN MUTATED                                 0
  16P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  16P GAIN MUTATED                                               1
  16P GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  16P GAIN MUTATED                              0
  16P GAIN WILD-TYPE                            7
D28V9, multiclass
                                                    clus
vv                                                   16P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                14
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               86
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     6
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   16P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  79
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                208
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      13
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  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     4 114
  16P GAIN WILD-TYPE  17 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4  114
  16P GAIN WILD-TYPE   17  327
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                 17
  YES              114                327
[1] 2 2
[1] FALSE
D28V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    84   2   1   7
  16P GAIN WILD-TYPE 234   9   3  12
D28V12, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               84                234
  R1                2                  9
  R2                1                  3
  RX                7                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  1     2
  16P GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           5    97
  16P GAIN WILD-TYPE                        21   265
D28V13, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       5                 21
  WHITE                                          97                265
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  91
  16P GAIN WILD-TYPE   6 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   91
  16P GAIN WILD-TYPE    6  241
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               91                241
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    64  17
  16Q GAIN WILD-TYPE 257  65
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                81                322 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                17                 65 
$`16Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-5423 TCGA-38-4627 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 
        1523          151         1147          864          354          448 
TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-6147 TCGA-44-6775 TCGA-44-6778 
        1367         1280         1301          845          705         1864 
TCGA-44-6779 TCGA-44-7662 TCGA-44-A47A TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 
        1978          218          466          428          268          157 
TCGA-49-6744 TCGA-50-5933 TCGA-50-5935 TCGA-50-6597 TCGA-50-8460 TCGA-55-1592 
         890         2370          653         1015          105          701 
TCGA-55-1594 TCGA-55-6712 TCGA-55-6980 TCGA-55-7284 TCGA-55-7726 TCGA-55-7910 
        1178           24           67          121           39          197 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 TCGA-55-8206 TCGA-55-8512 
         100           43           26           15           46            3 
TCGA-55-8615 TCGA-55-A490 TCGA-55-A4DG TCGA-62-8398 TCGA-62-8402 TCGA-64-1676 
          15           48          162         1970         1445         1728 
TCGA-64-1679 TCGA-64-1681 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7764 
        1686         1968          174          422          202          414 
TCGA-69-7980 TCGA-71-6725 TCGA-73-4668 TCGA-73-4675 TCGA-75-7025 TCGA-75-7027 
         382           61          467           40         1967         1956 
TCGA-78-7145 TCGA-78-7154 TCGA-78-7163 TCGA-78-7542 TCGA-78-8640 TCGA-86-7701 
        1973         1948         1950         1952         1949           11 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 
         508           10          476          482           16           35 
TCGA-86-8668 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6840 TCGA-91-8497 TCGA-97-7547 
          45           10           30          372          174         1965 
TCGA-97-7553 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8025 
        1332          147           15          115          271          427 
TCGA-99-8033 TCGA-J2-A4AD TCGA-MN-A4N4 
         170          287          622 

$`16Q GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
         607          426         1369         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         365          913          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         761          730          457          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4628 TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
        1962         1492         1073         1357         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 
        1324         1429          400          741           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1130         1163         1036          190          722         1013 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
         863          383          723          328          302          704 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
         658         1938         1942          444          592          366 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         557         1970          882          535          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
          99          260          486          287          337          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 
         415           76         1932         1081         1421          999 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 
         896         1700          445          369          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        2174         2146          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5941 TCGA-50-5942 
         246          282          267         1091          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
         764          686          255         1986         1971          424 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         280         1479         1375           87            2          993 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        1239           25         1475         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1170           18           35            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
          40         1958           39           34           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          19           16           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 
          33           21            6            4           47           33 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          66          216           44           23           29           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 
           8           15          228            9          146          202 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
         536           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          42           29         1952            1           28            5 
TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V 
          47         1216         1289         2696         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 
        1246          910          628         1189         1126         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
          62         1305          864         1559          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-69-7761 
         610          573          427          385          141          186 
TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         690          165          230          184           70           89 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 
         100           77          129          214         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         912          800          131          164           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
         519         1970         1965         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 
        1093         1963         1202          760         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 
        1963         1221          678          215         1940         1934 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1937         1965         1972         1949         1944          327 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         881          994         1971         1981         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
        1965         1972          824         1959          630          422 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
        1968          591         1963          745         1963           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
          24          479          489         1955           19           26 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 
          34           18           15          455          405           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323         1940           60          310           79 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         417          842          224           35          492          197 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
          36           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
          34            2          568          377          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
         121          964         1932          775          181           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M2 
         107          182         1965           87          148          197 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
         392          459           44          154          114          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         238          578          435          116            6          285 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
         353         1946         1967         1951         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1957         1980         1951         1944         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                  1 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              2370               2696 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             414.0              490.5 
[1] "3.0 - 2370.0 (414.0)" "1.0 - 2696.0 (490.5)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  16Q GAIN MUTATED         2       24       21        11        11         14
  16Q GAIN WILD-TYPE       2       89      110        32        58         53
                    vv
clus                 STAGE IIIB STAGE IV
  16Q GAIN MUTATED            2        4
  16Q GAIN WILD-TYPE          9       19
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                 24                 89
  STAGE IB                 21                110
  STAGE IIA                11                 32
  STAGE IIB                11                 58
  STAGE IIIA               14                 53
  STAGE IIIB                2                  9
  STAGE IV                  4                 19
[1] 8 2
[1] 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    31  44  10   3
  16Q GAIN WILD-TYPE 112 215  30  15
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               31                112
  T2               44                215
  T3               10                 30
  T4                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                  N0  N1 N2+N3
  16Q GAIN MUTATED    55  18    14
  16Q GAIN WILD-TYPE 240  67    58
D29V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                  55                240
  N1                  18                 67
  N2+N3               14                 58
[1] 3 2
[1] 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 M1B  MX
  16Q GAIN MUTATED    62   3   0   1  22
  16Q GAIN WILD-TYPE 255  15   1   2  97
D29V6, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                62                255
  M1                 3                 15
  M1A                0                  1
  M1B                1                  2
  MX                22                 97
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    45  44
  16Q GAIN WILD-TYPE 203 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     45   44
  16Q GAIN WILD-TYPE  203  170
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               45                203
  MALE                 44                170
[1] 2 2
[1] FALSE
D29V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16Q GAIN MUTATED                            2
  16Q GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16Q GAIN MUTATED                                   8
  16Q GAIN WILD-TYPE                                85
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                   64
  16Q GAIN WILD-TYPE                                                230
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16Q GAIN MUTATED                                            1
  16Q GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  16Q GAIN MUTATED                                               6
  16Q GAIN WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  16Q GAIN MUTATED                                0
  16Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  16Q GAIN MUTATED                                    1
  16Q GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  16Q GAIN MUTATED                              0                             6
  16Q GAIN WILD-TYPE                            2                            13
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  16Q GAIN MUTATED                                 0
  16Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  16Q GAIN MUTATED                                               1
  16Q GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  16Q GAIN MUTATED                              0
  16Q GAIN WILD-TYPE                            7
D29V9, multiclass
                                                    clus
vv                                                   16Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               64
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     6
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   16Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                230
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      13
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  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     3  86
  16Q GAIN WILD-TYPE  18 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   86
  16Q GAIN WILD-TYPE   18  355
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 3                 18
  YES               86                355
[1] 2 2
[1] FALSE
D29V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    64   3   1   5
  16Q GAIN WILD-TYPE 254   8   3  14
D29V12, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               64                254
  R1                3                  8
  R2                1                  3
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  1     2
  16Q GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           3    73
  16Q GAIN WILD-TYPE                        23   289
D29V13, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       3                 23
  WHITE                                          73                289
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  68
  16Q GAIN WILD-TYPE   6 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   68
  16Q GAIN WILD-TYPE    6  264
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               68                264
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    52  16
  17P GAIN WILD-TYPE 269  66
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                68                335 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                 66 
$`17P GAIN MUTATED`
TCGA-05-4382 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4432 TCGA-35-5375 
         607         1431         1997          455          761          264 
TCGA-38-4628 TCGA-44-2668 TCGA-44-3396 TCGA-44-6148 TCGA-44-6777 TCGA-44-7667 
        1492          246         1130          704         1942          557 
TCGA-44-A479 TCGA-49-6742 TCGA-50-5930 TCGA-50-5935 TCGA-55-1595 TCGA-55-5899 
         486          445          282          653         1479           87 
TCGA-55-6642 TCGA-55-6971 TCGA-55-7815 TCGA-55-7907 TCGA-55-7995 TCGA-55-8094 
         993           25           54           16            5            4 
TCGA-55-8207 TCGA-55-8302 TCGA-55-8507 TCGA-55-8615 TCGA-55-8620 TCGA-55-A494 
          66           23            8           15           66            5 
TCGA-55-A4DG TCGA-62-8398 TCGA-62-A471 TCGA-64-1677 TCGA-67-3772 TCGA-69-7973 
         162         1970         1246          628          573          230 
TCGA-69-7980 TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
         382           61          800          467           40          164 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7154 TCGA-78-7167 TCGA-78-7220 TCGA-78-8662 
        1950         1093         1948         1937         1965         1964 
TCGA-86-7713 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8585 TCGA-86-8669 
         422          508           10           24           35           34 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-95-7043 TCGA-97-8177 
          30          323           79          417            2          147 
TCGA-97-8179 TCGA-97-8552 TCGA-99-8032 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N5 
          15          115           44          116          285          353 
TCGA-MP-A4SV TCGA-MP-A4T9 
        1946         1980 

$`17P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 
        1523          426         1369         1126         1947          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
         610         1958          912          365          913          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
         791          791          761          730          457          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         882          670           30           62           14          225 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 
         182         1952         1962         1147          864         1073 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
         354         1357          448         1971          133         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1429          400         1367          741         1280         1301 
TCGA-44-2666 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
          97         1163         1036          190          722         1013 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         863          383          723          328          302          845 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         658          705         1938         1864         1978          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         592          366          218         1970          882          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B 
         719          385           99          260          466          287 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         337          351          415           76         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896          157 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
        1700          369          890          522          354         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2146          455          785          944         1499          246 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
         267         1091         2370          567          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         686         1015          255          105         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 
         424          280          701         1178         1375            2 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
          24         1239         1475           67         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        2151         1170           18           35          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40         1958           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          34           24           19          197           21            3 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
          31           33           21          100            6           43 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8299 
          26           47           15           33           46          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          44           29           11           15          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
           3          146          202          536           48           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
         106           33           42           29           48         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
           1           28           47         1216         1289         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
        1445         2067         2199          910         1728         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1686         1126         1968         1959           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 
         864         1559          866           31          610          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         690          414          165          184           70           89 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 
         100           77          129          214         1600          711 
TCGA-73-4662 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 
         912          131           38          621          519         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
        1967         1956         1965         1973         1988         1944 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1963         1202          760         1957         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1221          678          215         1940         1950         1934 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1972         1949         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 
         994         1949         1971         1981         1954         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
        1972          824         1959           11          630         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
         591         1963          745         1963           13          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
         489          476          482           16         1955           19 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          26           45           18           15          455          405 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          10           14           39         1940           60          310 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         372          842          224           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         174           36           44          218          297          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
         186           34          568          377          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         121          964         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
         181           22          107          182         1965           87 
TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         148          197          271          392          427          459 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         170          154          114          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T2 
         578          435            6          622         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1954         1957         1951         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                  1 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1997               2696 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               338                489 
[1] "2.0 - 1997.0 (338.0)" "1.0 - 2696.0 (489.0)"
[1] "hr=" "1.8"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  17P GAIN MUTATED         2       15       22         8         9         13
  17P GAIN WILD-TYPE       2       98      109        35        60         54
                    vv
clus                 STAGE IIIB STAGE IV
  17P GAIN MUTATED            4        5
  17P GAIN WILD-TYPE          7       18
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                 15                 98
  STAGE IB                 22                109
  STAGE IIA                 8                 35
  STAGE IIB                 9                 60
  STAGE IIIA               13                 54
  STAGE IIIB                4                  7
  STAGE IV                  5                 18
[1] 8 2
[1] 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    20  48   5   4
  17P GAIN WILD-TYPE 123 211  35  14
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               20                123
  T2               48                211
  T3                5                 35
  T4                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                  N0  N1 N2+N3
  17P GAIN MUTATED    44  17    16
  17P GAIN WILD-TYPE 251  68    56
D30V5, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                  44                251
  N1                  17                 68
  N2+N3               16                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  17P GAIN MUTATED    55   3   0   2  18
  17P GAIN WILD-TYPE 262  15   1   1 101
D30V6, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                55                262
  M1                 3                 15
  M1A                0                  1
  M1B                2                  1
  MX                18                101
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    35  43
  17P GAIN WILD-TYPE 213 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     35   43
  17P GAIN WILD-TYPE  213  171
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               35                213
  MALE                 43                171
[1] 2 2
[1] FALSE
D30V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17P GAIN MUTATED                            2
  17P GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17P GAIN MUTATED                                  16
  17P GAIN WILD-TYPE                                77
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                   51
  17P GAIN WILD-TYPE                                                243
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17P GAIN MUTATED                                            0
  17P GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  17P GAIN MUTATED                                               1
  17P GAIN WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  17P GAIN MUTATED                                1
  17P GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  17P GAIN MUTATED                                    1
  17P GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  17P GAIN MUTATED                              1                             2
  17P GAIN WILD-TYPE                            1                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  17P GAIN MUTATED                                 0
  17P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  17P GAIN MUTATED                                               2
  17P GAIN WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  17P GAIN MUTATED                              1
  17P GAIN WILD-TYPE                            6
D30V9, multiclass
                                                    clus
vv                                                   17P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                16
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               51
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   17P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                243
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     6  72
  17P GAIN WILD-TYPE  15 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      6   72
  17P GAIN WILD-TYPE   15  369
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 6                 15
  YES               72                369
[1] 2 2
[1] FALSE
D30V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    57   0   0   6
  17P GAIN WILD-TYPE 261  11   4  13
D30V12, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               57                261
  R1                0                 11
  R2                0                  4
  RX                6                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  1     2
  17P GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           2    62
  17P GAIN WILD-TYPE                        24   300
D30V13, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       2                 24
  WHITE                                          62                300
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  57
  17P GAIN WILD-TYPE   7 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   57
  17P GAIN WILD-TYPE    7  275
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               57                275
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   123  29
  17Q GAIN WILD-TYPE 198  53
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               152                251 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                29                 53 
$`17Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4398 TCGA-05-4410 TCGA-05-4415 
        1523          607         1369         1431         1958         1997 
TCGA-05-4417 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         455          913          669          791          761          761 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4632 TCGA-44-2668 TCGA-44-3396 TCGA-44-3919 
        1492          864         1357          246         1130          190 
TCGA-44-6144 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7661 TCGA-44-7662 
         723          704          705         1942          366          218 
TCGA-44-7667 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         557          882          385           99          260          486 
TCGA-44-A47B TCGA-49-4501 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         287         1421          445          369          890          522 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 
         282          267         2370          653          567          764 
TCGA-50-6597 TCGA-53-7813 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6971 
        1015          424         1479           87          993           25 
TCGA-55-7281 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
          18           34           54           19           16           21 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 TCGA-55-8094 TCGA-55-8205 TCGA-55-8207 
          31            5          100            4           33           66 
TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
          23            8          228          202           15           48 
TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DG 
          66           29           48         1952            5          162 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A471 TCGA-64-1677 TCGA-64-5774 TCGA-67-3770 
        1970         1445         1246          628         1959           31 
TCGA-67-3772 TCGA-67-6215 TCGA-69-7760 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         573          174          202          230          184           70 
TCGA-69-7980 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
         382           61         1600          912          800          467 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-78-7145 TCGA-78-7147 
          40          164          519         1970         1973         1950 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 
        1093         1948         1221          215         1937         1965 
TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 
         327         1952          994         1949         1954         1964 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 
        1959          630          422          591          508           10 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
          24          479          482           19           35           45 
TCGA-86-8669 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 
          34           30           14          323           79          417 
TCGA-91-6848 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
         224          127          186           34            2          568 
TCGA-95-7944 TCGA-97-7553 TCGA-97-7554 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         377         1332          775           87          147           15 
TCGA-97-8547 TCGA-97-8552 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A443 
         148          115          427           44          170          116 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T8 
         285          622          353         1946         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TE 
        1980         1970 

$`17Q GAIN WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 TCGA-05-4420 
         426         1126         1947          578          610          912 
TCGA-05-4422 TCGA-05-4426 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
         365          791          730          457          151          882 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
         670           30           62           14          225          182 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 
         264         1952         1962         1147         1073          354 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
         448         1971          133         1324         1429          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3398 
        1367          741         1280         1301           97         1163 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 
        1036          722         1013          863          383          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 
         302          845          658         1938         1864         1978 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47A 
         444          592         1970          535          719          466 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         337          351          415           76         1932         1081 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896          157         1700 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         354         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5932 TCGA-50-5942 TCGA-50-5946 TCGA-50-7109 
        1499          246         1091          883          686          255 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
         105         1986         1971          280          701         1178 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 
        1375            2           24         1239         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 
        1826         1233         2151         1170           35          121 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
           6            4           95           40         1958           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7910 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 
          39           24          197            3           33           21 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
           6           43           26           47           15           46 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8511 
         216           44           29           11           15            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
           3          146          536           49          106           33 
TCGA-55-A48Y TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 
          42            1           28           47         1216         1289 
TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
        2696         2067         2199          910         1728         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1686         1126         1968           62         1305          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 
        1559          866          610          427          385          141 
TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 
         422          186          690          414          165           89 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 TCGA-73-4670 
         100           77          129          214          711          131 
TCGA-73-4677 TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
          38          621         1967         1956         1965         1988 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 
        1944         1963         1202          760         1957         1961 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
        1963          678         1940         1950         1934         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 TCGA-80-5607 
        1949         1944          881         1971         1981         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
        1972          824           11         1968         1963          745 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 
        1963           13          489          476           16         1955 
TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          26           18           15          455          405           10 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 
          39         1940           60          310          372          842 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          35          492          197          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
         218          297          477          476          121          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1965         1932          181           22          107          182 
TCGA-97-8174 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-J2-8192 
        1965          197          271          392          459          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A444 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC 
           6         1967         1951         1954         1951         1944 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                  1 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              2370               2696 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               423                489 
[1] "2.0 - 2370.0 (423.0)" "1.0 - 2696.0 (489.0)"
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  17Q GAIN MUTATED         2       34       51        18        24         29
  17Q GAIN WILD-TYPE       2       79       80        25        45         38
                    vv
clus                 STAGE IIIB STAGE IV
  17Q GAIN MUTATED            7       11
  17Q GAIN WILD-TYPE          4       12
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                 34                 79
  STAGE IB                 51                 80
  STAGE IIA                18                 25
  STAGE IIB                24                 45
  STAGE IIIA               29                 38
  STAGE IIIB                7                  4
  STAGE IV                 11                 12
[1] 8 2
[1] 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    45 106  16   7
  17Q GAIN WILD-TYPE  98 153  24  11
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               45                 98
  T2              106                153
  T3               16                 24
  T4                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                  N0  N1 N2+N3
  17Q GAIN MUTATED   106  33    33
  17Q GAIN WILD-TYPE 189  52    39
D31V5, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                 106                189
  N1                  33                 52
  N2+N3               33                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  17Q GAIN MUTATED   124   9   0   2  41
  17Q GAIN WILD-TYPE 193   9   1   1  78
D31V6, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               124                193
  M1                 9                  9
  M1A                0                  1
  M1B                2                  1
  MX                41                 78
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    95  81
  17Q GAIN WILD-TYPE 153 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     95   81
  17Q GAIN WILD-TYPE  153  133
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               95                153
  MALE                 81                133
[1] 2 2
[1] FALSE
D31V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17Q GAIN MUTATED                            5
  17Q GAIN WILD-TYPE                          8
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17Q GAIN MUTATED                                  37
  17Q GAIN WILD-TYPE                                56
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                  117
  17Q GAIN WILD-TYPE                                                177
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17Q GAIN MUTATED                                            1
  17Q GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  17Q GAIN MUTATED                                               4
  17Q GAIN WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  17Q GAIN MUTATED                                2
  17Q GAIN WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  17Q GAIN MUTATED                                    2
  17Q GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  17Q GAIN MUTATED                              1                             3
  17Q GAIN WILD-TYPE                            1                            16
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  17Q GAIN MUTATED                                 0
  17Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  17Q GAIN MUTATED                                               3
  17Q GAIN WILD-TYPE                                             1
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  17Q GAIN MUTATED                              1
  17Q GAIN WILD-TYPE                            6
D31V9, multiclass
                                                    clus
vv                                                   17Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              117
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   17Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                177
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      16
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       1
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     8 168
  17Q GAIN WILD-TYPE  13 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      8  168
  17Q GAIN WILD-TYPE   13  273
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 8                 13
  YES              168                273
[1] 2 2
[1] FALSE
D31V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED   116   4   2  13
  17Q GAIN WILD-TYPE 202   7   2   6
D31V12, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0              116                202
  R1                4                  7
  R2                2                  2
  RX               13                  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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  1     3
  17Q GAIN WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           7   138
  17Q GAIN WILD-TYPE                        19   224
D31V13, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                       7                 19
  WHITE                                         138                224
[1] 4 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     3 120
  17Q GAIN WILD-TYPE   4 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3  120
  17Q GAIN WILD-TYPE    4  212
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              120                212
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    63  16
  18P GAIN WILD-TYPE 258  66
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                79                324 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                16                 66 
$`18P GAIN MUTATED`
TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 TCGA-05-5428 
        1958         1997          912          913          761          670 
TCGA-35-4122 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-6144 TCGA-44-6146 
         225          400         1367         1280          723          302 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-49-6761 TCGA-50-5068 
         719          385           99          466          354         1499 
TCGA-50-5931 TCGA-50-7109 TCGA-53-7813 TCGA-55-1595 TCGA-55-6980 TCGA-55-7907 
         267          255          424         1479           67           16 
TCGA-55-7994 TCGA-55-8089 TCGA-55-8096 TCGA-55-8508 TCGA-55-8511 TCGA-55-8615 
          31          100           47           15            9           15 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
           5           47          162         1970         2696         1445 
TCGA-64-1676 TCGA-64-1677 TCGA-64-5775 TCGA-64-5779 TCGA-69-7764 TCGA-69-7973 
        1728          628           62          864          414          230 
TCGA-69-7980 TCGA-69-8253 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
         382          100          912          467           40          164 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7155 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 
        1950         1944         1957         1949          327         1952 
TCGA-78-8662 TCGA-86-7713 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 
        1964          422          508          745           10           24 
TCGA-86-8075 TCGA-86-8359 TCGA-86-8585 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 
         479           26           35           30         1940          310 
TCGA-91-6840 TCGA-91-8499 TCGA-95-7944 TCGA-95-7947 TCGA-97-7546 TCGA-97-7554 
         372           36          377          477          964          775 
TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 
          87           15          115          116            6          622 
TCGA-MP-A4TK 
        1971 

$`18P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 
        1431          578          610          455          365          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
         791          791          761          730          457          151 
TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 
         882           30           62           14          182          264 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        1952         1962         1147         1492          864         1073 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
         354         1357          448         1971          133         1324 
TCGA-44-2656 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
        1429          741         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
        1163         1036          190          722         1013          863 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         383          328          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
        1938         1942         1864         1978          444          592 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         366          218          557         1970          882          535 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         260          486          287          337          351          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
          76         1932         1081         1421          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         268          896          157         1700          445          369 
TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         890          522         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         944          246          282         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-8460 
         567          883          764          686         1015          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
        1986         1971          280          701         1178         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
          87            2          993           24         1239           25 
TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
        1475         1826         1233         2151         1170           18 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          35          121            6            4           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        1958           39           39           34           24           54 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
          19          197           21            3            5           33 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
          21            6           43           26            4           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
          29           11            8          228            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         202          536           48           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
          33           42           29           48         1952            1 
TCGA-55-A493 TCGA-62-8395 TCGA-62-8397 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
          28         1216         1289         2067         2199         1246 
TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
         910         1189         1686         1126         1968         1959 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1305         1559          866           31          610          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         427          385          174          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         186          690          165          184           70           89 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
          77          129          214           61         1600          711 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 
         800          131           38          621          519         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7149 
        1967         1956         1965         1973         1988         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
        1963         1202          760         1948         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1221          678          215         1940         1950         1934 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 
        1937         1965         1972         1944          881          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 
        1949         1971         1981         1954         1965         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
         824         1959           11          630         1968          591 
TCGA-86-7954 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        1963         1963           13          489          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          16         1955           19           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
          15          455          405           10           14           39 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
         323           60           79          417          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
          35          492          197          174           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
         297          127          186           34            2          568 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
         476          121         1965         1932         1332          181 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 
          22          107          182         1965          147          148 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
         197          271          392          427          459           44 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         170          154          114          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         578          435          285          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1951         1954         1954         1957         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1944         1970         1970          142         1955         1490 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                  1 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              2696               2370 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             400.0              487.5 
[1] "5.0 - 2696.0 (400.0)" "1.0 - 2370.0 (487.5)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  18P GAIN MUTATED         3       22       24         9        12         15
  18P GAIN WILD-TYPE       1       91      107        34        57         52
                    vv
clus                 STAGE IIIB STAGE IV
  18P GAIN MUTATED            2        1
  18P GAIN WILD-TYPE          9       22
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   3                  1
  STAGE IA                 22                 91
  STAGE IB                 24                107
  STAGE IIA                 9                 34
  STAGE IIB                12                 57
  STAGE IIIA               15                 52
  STAGE IIIB                2                  9
  STAGE IV                  1                 22
[1] 8 2
[1] 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    31  47   7   3
  18P GAIN WILD-TYPE 112 212  33  15
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               31                112
  T2               47                212
  T3                7                 33
  T4                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                  N0  N1 N2+N3
  18P GAIN MUTATED    58  15    14
  18P GAIN WILD-TYPE 237  70    58
D32V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                  58                237
  N1                  15                 70
  N2+N3               14                 58
[1] 3 2
[1] 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 M1B  MX
  18P GAIN MUTATED    64   1   0   0  23
  18P GAIN WILD-TYPE 253  17   1   3  96
D32V6, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                64                253
  M1                 1                 17
  M1A                0                  1
  M1B                0                  3
  MX                23                 96
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    44  44
  18P GAIN WILD-TYPE 204 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     44   44
  18P GAIN WILD-TYPE  204  170
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               44                204
  MALE                 44                170
[1] 2 2
[1] FALSE
D32V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18P GAIN MUTATED                            4
  18P GAIN WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18P GAIN MUTATED                                  15
  18P GAIN WILD-TYPE                                78
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                   55
  18P GAIN WILD-TYPE                                                239
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18P GAIN MUTATED                                            0
  18P GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  18P GAIN MUTATED                                               5
  18P GAIN WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  18P GAIN MUTATED                                1
  18P GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  18P GAIN MUTATED                                    1
  18P GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  18P GAIN MUTATED                              1                             3
  18P GAIN WILD-TYPE                            1                            16
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  18P GAIN MUTATED                                 0
  18P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  18P GAIN MUTATED                                               2
  18P GAIN WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  18P GAIN MUTATED                              1
  18P GAIN WILD-TYPE                            6
D32V9, multiclass
                                                    clus
vv                                                   18P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               55
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   18P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                239
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      16
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     3  85
  18P GAIN WILD-TYPE  18 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3   85
  18P GAIN WILD-TYPE   18  356
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 3                 18
  YES               85                356
[1] 2 2
[1] FALSE
D32V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    62   2   0   5
  18P GAIN WILD-TYPE 256   9   4  14
D32V12, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               62                256
  R1                2                  9
  R2                0                  4
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  1     1
  18P GAIN WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           2    74
  18P GAIN WILD-TYPE                        24   288
D32V13, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       2                 24
  WHITE                                          74                288
[1] 4 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     0  67
  18P GAIN WILD-TYPE   7 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   67
  18P GAIN WILD-TYPE    7  265
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               67                265
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    50   9
  18Q GAIN WILD-TYPE 271  73
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                59                344 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                 73 
$`18Q GAIN MUTATED`
TCGA-05-4390 TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 TCGA-35-4122 TCGA-44-2659 
        1126         1958         1997          912          225         1367 
TCGA-44-6144 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-7672 TCGA-44-8119 
         723         1864          592          557          719           99 
TCGA-44-A47A TCGA-49-4510 TCGA-49-6761 TCGA-50-5931 TCGA-53-7813 TCGA-55-1595 
         466          896          354          267          424         1479 
TCGA-55-7907 TCGA-55-8089 TCGA-55-8096 TCGA-55-8508 TCGA-55-8511 TCGA-55-8615 
          16          100           47           15            9           15 
TCGA-55-8620 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 
          66            5           47          162         1970         2696 
TCGA-62-8402 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-5779 TCGA-69-7764 
        1445         1728          628         1189          864          414 
TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-71-6725 TCGA-73-4668 TCGA-73-4675 
         230          382          100           61          467           40 
TCGA-73-4676 TCGA-78-7148 TCGA-78-7167 TCGA-78-7542 TCGA-86-7713 TCGA-86-7955 
         164         1944         1937         1952          422          508 
TCGA-86-8075 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-A4D0 TCGA-91-6831 
         479           19           26           35           30          310 
TCGA-91-8499 TCGA-97-7546 TCGA-97-7554 TCGA-97-8175 TCGA-97-8552 
          36          964          775           87          115 

$`18Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 
        1523          607          426         1369         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
         578          610          455          365          913          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         791          791          761          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         151          882          670           30           62           14 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         182          264         1952         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         864         1073          354         1357          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
         133         1324         1429          400          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 
         190          722         1013          863          383          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         302          845          704          658          705         1938 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
        1942         1978          444          366          218         1970 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
         882          535          385          260          486          287 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         337          351          415           76         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
        1421          428          999          268          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 
         445          369          890          522         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         686         1015          255          105         1986         1971 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
         280          701         1178         1375           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
         993           24         1239           25         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1826         1233         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
          39           39           34           24           54           19 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
         197           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
          21            6           43           26            4           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
          29           11            8          228            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
         202          536           48           49          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          42           29           48         1952            1           28 
TCGA-62-8395 TCGA-62-8397 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1216         1289         2067         2199         1246          910 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1686         1126         1968         1959           62         1305 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        1559          866           31          610          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 
         690          165          184           70           89           77 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         129          214         1600          711          912          800 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         131           38          621          519         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
        1956         1965         1973         1988         1950         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1963         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1963         1221          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1934         1965         1972         1949         1944          327 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
         881          994         1949         1971         1981         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1964         1965         1972          824         1959           11 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
         630         1968          591         1963          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        1963           13           24          489          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          16         1955           45           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         455          405           10           14           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
        1940           60           79          417          372          842 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
         224           35          492          197          174           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         218          297          127          186           34            2 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 
         568          377          477          476          121         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932         1332          181           22          107          182 
TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 
        1965          147           15          148          197          271 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         392          427          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         116            6          285          622          353         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1967         1951         1954         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1951         1944         1970         1970          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                  1 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              2696               2370 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             422.0              476.5 
[1] "5.0 - 2696.0 (422.0)" "1.0 - 2370.0 (476.5)"
[1] "hr=" "1.1"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  18Q GAIN MUTATED         2       12       19         6         7         12
  18Q GAIN WILD-TYPE       2      101      112        37        62         55
                    vv
clus                 STAGE IIIB STAGE IV
  18Q GAIN MUTATED            2        3
  18Q GAIN WILD-TYPE          9       20
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                 12                101
  STAGE IB                 19                112
  STAGE IIA                 6                 37
  STAGE IIB                 7                 62
  STAGE IIIA               12                 55
  STAGE IIIB                2                  9
  STAGE IV                  3                 20
[1] 8 2
[1] 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    18  38   5   2
  18Q GAIN WILD-TYPE 125 221  35  16
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               18                125
  T2               38                221
  T3                5                 35
  T4                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                  N0  N1 N2+N3
  18Q GAIN MUTATED    41  10    12
  18Q GAIN WILD-TYPE 254  75    60
D33V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                  41                254
  N1                  10                 75
  N2+N3               12                 60
[1] 3 2
[1] 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 M1B  MX
  18Q GAIN MUTATED    41   2   0   1  19
  18Q GAIN WILD-TYPE 276  16   1   2 100
D33V6, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                41                276
  M1                 2                 16
  M1A                0                  1
  M1B                1                  2
  MX                19                100
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    31  32
  18Q GAIN WILD-TYPE 217 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     31   32
  18Q GAIN WILD-TYPE  217  182
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               31                217
  MALE                 32                182
[1] 2 2
[1] FALSE
D33V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18Q GAIN MUTATED                            2
  18Q GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18Q GAIN MUTATED                                  10
  18Q GAIN WILD-TYPE                                83
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                   39
  18Q GAIN WILD-TYPE                                                255
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18Q GAIN MUTATED                                            0
  18Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  18Q GAIN MUTATED                                               2
  18Q GAIN WILD-TYPE                                            17
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  18Q GAIN MUTATED                                1
  18Q GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  18Q GAIN MUTATED                                    1
  18Q GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  18Q GAIN MUTATED                              0                             5
  18Q GAIN WILD-TYPE                            2                            14
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  18Q GAIN MUTATED                                 0
  18Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  18Q GAIN MUTATED                                               2
  18Q GAIN WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  18Q GAIN MUTATED                              1
  18Q GAIN WILD-TYPE                            6
D33V9, multiclass
                                                    clus
vv                                                   18Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               39
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     5
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   18Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                255
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      17
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      14
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     2  61
  18Q GAIN WILD-TYPE  19 380
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   61
  18Q GAIN WILD-TYPE   19  380
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 2                 19
  YES               61                380
[1] 2 2
[1] FALSE
D33V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    39   1   0   6
  18Q GAIN WILD-TYPE 279  10   4  13
D33V12, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               39                279
  R1                1                 10
  R2                0                  4
  RX                6                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  1     2
  18Q GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           4    51
  18Q GAIN WILD-TYPE                        22   311
D33V13, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       4                 22
  WHITE                                          51                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"
D33V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  52
  18Q GAIN WILD-TYPE   7 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   52
  18Q GAIN WILD-TYPE    7  280
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               52                280
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    25   2
  19P GAIN WILD-TYPE 296  80
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                27                376 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 80 
$`19P GAIN MUTATED`
TCGA-05-4390 TCGA-05-4424 TCGA-44-2662 TCGA-44-2665 TCGA-44-3918 TCGA-44-6147 
        1126          913         1280         1301         1036          845 
TCGA-44-A47A TCGA-44-A47F TCGA-50-5049 TCGA-53-7624 TCGA-55-7907 TCGA-55-8615 
         466          337         2146         1986           16           15 
TCGA-55-8620 TCGA-62-8399 TCGA-69-7973 TCGA-69-8253 TCGA-73-4675 TCGA-78-7154 
          66         2696          230          100           40         1948 
TCGA-86-8359 TCGA-86-8585 TCGA-95-7944 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 
          26           35          377          775          181          182 
TCGA-97-8175 TCGA-97-8179 TCGA-MN-A4N4 
          87           15          622 

$`19P GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 
        1523          607          426         1369         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         365          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         730          457          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1357          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         400         1367          741           97          246         1130 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1163          190          722         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         723          328          302          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
        1938         1942         1864         1978          444          592 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         366          218          557         1970          882          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
         719          385           99          260          486          287 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         351          415           76         1932         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
         445          369          890          522          354         2174 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         267         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 
         764          686         1015          255          105         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
         424          280          701         1178         1479         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
          87            2          993           24         1239           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        1475           67         1826         1233         2151         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
          18           35          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          54           19          197           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33           21          100            6           43 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
          26            4           47           15           33           46 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          66          216           44           23           29           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
           8           15          228            9            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
         202          536           48           49          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          42           29           48         1952            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           5           47          162         1216         1289         1970 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
        1445         2067         2199         1246          910         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
         628         1189         1686         1126         1968         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
          62         1305          864         1559          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         610          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 
         184           70           89          382           77          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         214           61         1600          711          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         467          131          164           38          621          519 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
        1970         1967         1956         1965         1973         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1950         1944         1093         1963         1202          760 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1957         1961         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        1940         1950         1934         1937         1965         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1949         1944          327          881         1952          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
        1949         1971         1981         1954         1964         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
        1972          824         1959           11          630          422 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
        1968          591         1963          508          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        1963           13           24          479          489          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 
         482           16         1955           19           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          18           15          455          405           10           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          14           39          323         1940           60          310 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
          79          417          372          842          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          197          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
         297          127          186           34            2          568 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         477          476          121          964         1965         1932 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 
        1332           22          107         1965          147          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         115          197          271          392          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
          44          170          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         238          578          435          116            6          285 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
         353         1946         1967         1951         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1957         1980         1951         1944         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                15                  1 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              2696               2370 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             377.0              471.5 
[1] "15.0 - 2696.0 (377.0)" "1.0 - 2370.0 (471.5)" 
[1] "hr=" "4.4"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  19P GAIN MUTATED         0        7        8         1         4          7
  19P GAIN WILD-TYPE       4      106      123        42        65         60
                    vv
clus                 STAGE IIIB STAGE IV
  19P GAIN MUTATED            0        2
  19P GAIN WILD-TYPE         11       21
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                  7                106
  STAGE IB                  8                123
  STAGE IIA                 1                 42
  STAGE IIB                 4                 65
  STAGE IIIA                7                 60
  STAGE IIIB                0                 11
  STAGE IV                  2                 21
[1] 8 2
[1] 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     8  15   6   0
  19P GAIN WILD-TYPE 135 244  34  18
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                8                135
  T2               15                244
  T3                6                 34
  T4                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                  N0  N1 N2+N3
  19P GAIN MUTATED    16   6     6
  19P GAIN WILD-TYPE 279  79    66
D34V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                  16                279
  N1                   6                 79
  N2+N3                6                 66
[1] 3 2
[1] 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 M1B  MX
  19P GAIN MUTATED    22   1   0   1   5
  19P GAIN WILD-TYPE 295  17   1   2 114
D34V6, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                22                295
  M1                 1                 17
  M1A                0                  1
  M1B                1                  2
  MX                 5                114
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    13  16
  19P GAIN WILD-TYPE 235 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     13   16
  19P GAIN WILD-TYPE  235  198
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               13                235
  MALE                 16                198
[1] 2 2
[1] FALSE
D34V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19P GAIN MUTATED                            2
  19P GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19P GAIN MUTATED                                   4
  19P GAIN WILD-TYPE                                89
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                   17
  19P GAIN WILD-TYPE                                                277
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19P GAIN MUTATED                                            0
  19P GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  19P GAIN MUTATED                                               0
  19P GAIN WILD-TYPE                                            19
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  19P GAIN MUTATED                                0
  19P GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  19P GAIN MUTATED                                    1
  19P GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  19P GAIN MUTATED                              0                             2
  19P GAIN WILD-TYPE                            2                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  19P GAIN MUTATED                                 1
  19P GAIN WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  19P GAIN MUTATED                                               2
  19P GAIN WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  19P GAIN MUTATED                              0
  19P GAIN WILD-TYPE                            7
D34V9, multiclass
                                                    clus
vv                                                   19P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               17
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     0
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   19P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                277
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      19
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        7
[1] 12  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     1  28
  19P GAIN WILD-TYPE  20 413
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   28
  19P GAIN WILD-TYPE   20  413
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 1                 20
  YES               28                413
[1] 2 2
[1] FALSE
D34V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    17   1   0   1
  19P GAIN WILD-TYPE 301  10   4  18
D34V12, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               17                301
  R1                1                 10
  R2                0                  4
  RX                1                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     0
  19P GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           2    24
  19P GAIN WILD-TYPE                        24   338
D34V13, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       2                 24
  WHITE                                          24                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"
D34V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  24
  19P GAIN WILD-TYPE   6 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   24
  19P GAIN WILD-TYPE    6  308
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               24                308
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    49  10
  19Q GAIN WILD-TYPE 272  72
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                59                344 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                 72 
$`19Q GAIN MUTATED`
TCGA-05-4390 TCGA-05-4424 TCGA-35-4122 TCGA-35-5375 TCGA-38-4631 TCGA-44-2662 
        1126          913          225          264          354         1280 
TCGA-44-3918 TCGA-44-6144 TCGA-44-6147 TCGA-44-6776 TCGA-44-7660 TCGA-44-7669 
        1036          723          845         1938          592         1970 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-49-4510 TCGA-49-6743 
         466          287          337          415          896          369 
TCGA-50-5049 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-6971 TCGA-55-7907 TCGA-55-8092 
        2146         1986          280           25           16           26 
TCGA-55-8302 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-62-8399 TCGA-64-5778 
          23          536           15           66         2696         1305 
TCGA-64-5781 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 
        1559          690          414          230          382          100 
TCGA-73-4675 TCGA-78-7150 TCGA-78-7154 TCGA-86-7713 TCGA-86-8055 TCGA-86-8358 
          40         1963         1948          422           10           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8673 TCGA-91-6830 TCGA-95-7043 TCGA-95-7944 
          26           35          455           60            2          377 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8179 TCGA-99-8025 
         775          181          182         1965           15          427 
TCGA-L9-A443 TCGA-MN-A4N4 TCGA-MP-A4T7 TCGA-MP-A4TC TCGA-MP-A4TH 
         116          622         1954         1944          142 

$`19Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 
        1523          607          426         1369         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         365          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         730          457          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
          62           14          182         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
        1492          864         1073         1357          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
        1301           97          246         1130         1163          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
         722         1013          863          383          328          302 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
         704          658          705         1942         1864         1978 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 
         444          366          218          557          882          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G 
         719          385           99          260          486          351 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
          76         1932         1081         1421          428          999 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
         268          157         1700          445          890          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
         354         2174          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         246          282          267         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 
         567          883          764          686         1015          255 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
         105         1971          424          701         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
        1375           87            2          993           24         1239 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        1475           67         1826         1233         2151         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
          18           35          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          54           19          197           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33           21          100            6           43 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           4           47           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
         216           44           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 
         228            9            3          146          202           48 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          49          106           33           42           29           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1952            1           28            5           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
        1216         1289         1970         1445         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        1246          910         1728          628         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 
        1126         1968         1959           62          864          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
          31          610          573          427          385          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 
         141          422          202          186          165          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
          70           89           77          129          214           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        1600          711          912          800          467          131 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         164           38          621          519         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1956         1965         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1093         1202          760         1957         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1221          678          215         1940         1950         1934 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1937         1965         1972         1949         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881         1952          994         1949         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
          11          630         1968          591         1963          508 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
         745         1963           13           24          479          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 TCGA-86-8669 
         476          482           16         1955           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          18           15          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          39          323         1940          310           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         372          842          224           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         174           36           44          218          297          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
         186           34          568          477          476          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 
         964         1965         1932         1332           22          107 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
          87          147          148          115          197          271 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         392          459           44          170          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 
         287          282          238          578          435            6 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         285          353         1946         1967         1951         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
        1957         1980         1951         1970         1970         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                  1 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              2696               2370 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             414.0              480.5 
[1] "2.0 - 2696.0 (414.0)" "1.0 - 2370.0 (480.5)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  19Q GAIN MUTATED         1       16       20         7         6         13
  19Q GAIN WILD-TYPE       3       97      111        36        63         54
                    vv
clus                 STAGE IIIB STAGE IV
  19Q GAIN MUTATED            0        3
  19Q GAIN WILD-TYPE         11       20
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 16                 97
  STAGE IB                 20                111
  STAGE IIA                 7                 36
  STAGE IIB                 6                 63
  STAGE IIIA               13                 54
  STAGE IIIB                0                 11
  STAGE IV                  3                 20
[1] 8 2
[1] 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    21  35   9   0
  19Q GAIN WILD-TYPE 122 224  31  18
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               21                122
  T2               35                224
  T3                9                 31
  T4                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                  N0  N1 N2+N3
  19Q GAIN MUTATED    42  11    12
  19Q GAIN WILD-TYPE 253  74    60
D35V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                  42                253
  N1                  11                 74
  N2+N3               12                 60
[1] 3 2
[1] 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 M1B  MX
  19Q GAIN MUTATED    46   2   0   1  17
  19Q GAIN WILD-TYPE 271  16   1   2 102
D35V6, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                46                271
  M1                 2                 16
  M1A                0                  1
  M1B                1                  2
  MX                17                102
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    25  41
  19Q GAIN WILD-TYPE 223 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     25   41
  19Q GAIN WILD-TYPE  223  173
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               25                223
  MALE                 41                173
[1] 2 2
[1] FALSE
D35V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19Q GAIN MUTATED                            3
  19Q GAIN WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19Q GAIN MUTATED                                   9
  19Q GAIN WILD-TYPE                                84
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                   43
  19Q GAIN WILD-TYPE                                                251
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19Q GAIN MUTATED                                            0
  19Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  19Q GAIN MUTATED                                               2
  19Q GAIN WILD-TYPE                                            17
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  19Q GAIN MUTATED                                1
  19Q GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  19Q GAIN MUTATED                                    1
  19Q GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  19Q GAIN MUTATED                              0                             4
  19Q GAIN WILD-TYPE                            2                            15
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  19Q GAIN MUTATED                                 1
  19Q GAIN WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  19Q GAIN MUTATED                                               1
  19Q GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  19Q GAIN MUTATED                              1
  19Q GAIN WILD-TYPE                            6
D35V9, multiclass
                                                    clus
vv                                                   19Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               43
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   19Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                251
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      17
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      15
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     1  65
  19Q GAIN WILD-TYPE  20 376
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   65
  19Q GAIN WILD-TYPE   20  376
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 1                 20
  YES               65                376
[1] 2 2
[1] FALSE
D35V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    41   1   0   3
  19Q GAIN WILD-TYPE 277  10   4  16
D35V12, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               41                277
  R1                1                 10
  R2                0                  4
  RX                3                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     0
  19Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           5    54
  19Q GAIN WILD-TYPE                        21   308
D35V13, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                  6
  BLACK OR AFRICAN AMERICAN                       5                 21
  WHITE                                          54                308
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2  51
  19Q GAIN WILD-TYPE   5 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   51
  19Q GAIN WILD-TYPE    5  281
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               51                281
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   106  32
  20P GAIN WILD-TYPE 215  50
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               138                265 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                32                 50 
$`20P GAIN MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4417 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 
        1523         1369          455          913          761          761 
TCGA-05-5420 TCGA-05-5425 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4629 
         457          882          264         1952         1147          864 
TCGA-38-4631 TCGA-38-6178 TCGA-44-2657 TCGA-44-3918 TCGA-44-5644 TCGA-44-5645 
         354          448          400         1036          863          383 
TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-7660 
         723          845          658          705         1864          592 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
         218          557         1970          535          719           99 
TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 
         486          287          337          415           76         1081 
TCGA-49-4506 TCGA-49-4510 TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 
         999          896         2174         2146          944         1499 
TCGA-50-5931 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 TCGA-50-7109 TCGA-53-7813 
         267          653          567          686          255          424 
TCGA-55-1592 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 
         701         1375           87            2          993         1239 
TCGA-55-6972 TCGA-55-7284 TCGA-55-7574 TCGA-55-7724 TCGA-55-7726 TCGA-55-7995 
        1475          121           95         1958           39            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
          33           21           47           15           33           46 
TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
          23            8           15          202          536           15 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          29         1952           28            5           47          162 
TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 TCGA-64-5775 TCGA-67-3771 TCGA-67-3772 
        2696         1445          628           62          610          573 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
         690          414           70           89          382          100 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4677 TCGA-75-7027 
          61         1600          912          467           38         1956 
TCGA-75-7031 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7163 
        1965          760         1948         1957         1221         1950 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-83-5908 
        1937         1965         1949         1952         1949          824 
TCGA-86-7713 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8585 
         422          745           10           13          479           35 
TCGA-86-8669 TCGA-91-6829 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 
          34         1940          417          372          842           36 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7567 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 
          44          186          568          964         1332          181 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-99-8025 TCGA-MN-A4N1 
        1965           87           15          115          427          285 
TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK 
         353         1951         1954         1970         1970         1971 

$`20P GAIN WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         607          426         1126         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
         610         1958         1997          912          365          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
         791          791          730          151          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4628 
          62           14          225          182         1962         1492 
TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1073         1357         1971          133         1324         1429 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1367          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-6145 
        1130         1163          190          722         1013          328 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
         302          704         1938         1942         1978          444 
TCGA-44-7661 TCGA-44-7670 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47G 
         366          882          385          260          466          351 
TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
        1932         1421          428          268          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5051 
         445          369          890          522          354          455 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5942 
         785          246          282         1091         2370          883 
TCGA-50-5944 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
         764         1015          105         1986         1971          280 
TCGA-55-1594 TCGA-55-1595 TCGA-55-6712 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 
        1178         1479           24           25           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
        1233         2151         1170           18           35            6 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
           4           40           39           34           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          19           16          197           21            3           31 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8207 
         100            6           43           26            4           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 
         216           44           29           11          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
           3          146           48           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-62-8395 TCGA-62-8397 
          33           42           48            1         1216         1289 
TCGA-62-8398 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
        1970         2067         2199         1246          910         1728 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
        1189         1686         1126         1968         1959         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 
         864         1559          866           31          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 
         174          141          422          202          186          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 
         230          184           77          129          214          711 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 
         800          131           40          164          621          519 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1970         1967         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
        1093         1963         1202         1961         1963          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
         215         1940         1934         1972         1944          327 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         881          994         1971         1981         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
        1965         1972         1959           11          630         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 
         591         1963          508         1963           24          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         476          482           16         1955           19           26 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          45           18           15          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 
          30           14           39          323           60          310 
TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
          79          224           35          492          197          174 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 
         218          297          127           34            2          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 
         477          476          121         1965         1932          775 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M2 
          22          107          182          147          148          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         271          392          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
         116            6          622         1946         1967         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI 
        1957         1980         1951         1944          142         1955 
TCGA-MP-A5C7 
        1490 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                  1 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              2696               2370 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               562                435 
[1] "2.0 - 2696.0 (562.0)" "1.0 - 2370.0 (435.0)"
[1] "hr=" "1.4"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  20P GAIN MUTATED         3       41       51        12        22         19
  20P GAIN WILD-TYPE       1       72       80        31        47         48
                    vv
clus                 STAGE IIIB STAGE IV
  20P GAIN MUTATED            3        4
  20P GAIN WILD-TYPE          8       19
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   3                  1
  STAGE IA                 41                 72
  STAGE IB                 51                 80
  STAGE IIA                12                 31
  STAGE IIB                22                 47
  STAGE IIIA               19                 48
  STAGE IIIB                3                  8
  STAGE IV                  4                 19
[1] 8 2
[1] 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    47  94  11   3
  20P GAIN WILD-TYPE  96 165  29  15
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               47                 96
  T2               94                165
  T3               11                 29
  T4                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                  N0  N1 N2+N3
  20P GAIN MUTATED   107  24    19
  20P GAIN WILD-TYPE 188  61    53
D36V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                 107                188
  N1                  24                 61
  N2+N3               19                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  20P GAIN MUTATED    99   4   0   0  49
  20P GAIN WILD-TYPE 218  14   1   3  70
D36V6, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                99                218
  M1                 4                 14
  M1A                0                  1
  M1B                0                  3
  MX                49                 70
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    82  73
  20P GAIN WILD-TYPE 166 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     82   73
  20P GAIN WILD-TYPE  166  141
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               82                166
  MALE                 73                141
[1] 2 2
[1] FALSE
D36V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20P GAIN MUTATED                            4
  20P GAIN WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20P GAIN MUTATED                                  21
  20P GAIN WILD-TYPE                                72
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                  111
  20P GAIN WILD-TYPE                                                183
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20P GAIN MUTATED                                            1
  20P GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20P GAIN MUTATED                                               6
  20P GAIN WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  20P GAIN MUTATED                                0
  20P GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  20P GAIN MUTATED                                    2
  20P GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  20P GAIN MUTATED                              0                             7
  20P GAIN WILD-TYPE                            2                            12
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  20P GAIN MUTATED                                 0
  20P GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  20P GAIN MUTATED                                               2
  20P GAIN WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  20P GAIN MUTATED                              1
  20P GAIN WILD-TYPE                            6
D36V9, multiclass
                                                    clus
vv                                                   20P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              111
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     7
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   20P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  72
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                183
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      12
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     7 148
  20P GAIN WILD-TYPE  14 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7  148
  20P GAIN WILD-TYPE   14  293
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 7                 14
  YES              148                293
[1] 2 2
[1] FALSE
D36V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED    94   5   2   5
  20P GAIN WILD-TYPE 224   6   2  14
D36V12, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               94                224
  R1                5                  6
  R2                2                  2
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  1     3
  20P GAIN WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          14   119
  20P GAIN WILD-TYPE                        12   243
D36V13, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                      14                 12
  WHITE                                         119                243
[1] 4 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     1 116
  20P GAIN WILD-TYPE   6 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1  116
  20P GAIN WILD-TYPE    6  216
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              116                216
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   122  35
  20Q GAIN WILD-TYPE 199  47
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               157                246 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                35                 47 
$`20Q GAIN MUTATED`
TCGA-05-4389 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 
        1369          455          912          913          761          761 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
         457          151          882          264         1952         1147 
TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-44-2657 TCGA-44-3918 TCGA-44-5645 
         864          354          448          400         1036          383 
TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-7660 
         723          845          658          705         1864          592 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
         218          557         1970          882          535          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47F TCGA-44-A4SU TCGA-49-4494 
         385           99          486          337           76         1081 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 
         999          896          157          944         1499          267 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 TCGA-50-7109 TCGA-53-7813 TCGA-55-1592 
         653          567          686          255          424          701 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
        1178         1375            2          993           24         1239 
TCGA-55-6972 TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 
        1475          121         1958           39           16          197 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 
           5           33           26           47           33           46 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 
          23           11            8           15          202          536 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF 
          15           66           29         1952           28           47 
TCGA-55-A4DG TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 TCGA-64-1681 TCGA-64-5774 
         162         2696         1445          628         1968         1959 
TCGA-64-5775 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-69-7763 TCGA-69-7764 
          62         1559          610          573          690          414 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 
          70           89          382          100          129           61 
TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-75-6214 
        1600          800          467          131           38         1970 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 
        1956         1965          760         1948         1957         1221 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 
        1950         1937         1965         1972         1949         1952 
TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 TCGA-86-7713 TCGA-86-8054 TCGA-86-8055 
        1949         1954          824          422          745           10 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8279 TCGA-86-8585 TCGA-86-8669 TCGA-91-6829 
          13          479          482           35           34         1940 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 
          79          417          372          842          492           36 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 
          44          186           34            2          568          477 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         964         1332          181           87          147           15 
TCGA-97-8552 TCGA-99-8025 TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
         115          427          578            6          285          622 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF 
         353         1946         1951         1954         1970         1970 
TCGA-MP-A4TK 
        1971 

$`20Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
        1523          607          426         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 
         578          610         1958         1997          365          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         791          791          730          670           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4628 TCGA-38-4630 
          14          225          182         1962         1492         1073 
TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 
        1357         1971          133         1324         1429         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         741         1280         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6145 
        1163          190          722         1013          863          328 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
         302          704         1938         1942         1978          444 
TCGA-44-7661 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
         366          260          466          287          351          415 
TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 
        1932         1421          428          268         1700          445 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
         369          890          522          354         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
         455          785          246          282         1091         2370 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         883          764         1015          105         1986         1971 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 
         280         1479           87           25           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
        1233         2151         1170           18           35            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
           4           95           40           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8087 
          54           19           21            3           31           21 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8207 
         100            6           43            4           15           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
         216           44           29          228            9            3 
TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         146           48           49          106           33           42 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
          48            1            5         1216         1289         1970 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
        2067         2199         1246          910         1728         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 
        1686         1126         1305          864          866           31 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         427          385          174          141          422          202 
TCGA-69-7761 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8254 TCGA-69-A59K 
         186          165          230          184           77          214 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 
         711          912           40          164          621          519 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        1967         1973         1988         1950         1944         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 
        1963         1202         1961         1963          678          215 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1940         1934         1944          327          881          994 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 
        1971         1981         1964         1965         1972         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
          11          630         1968          591         1963          508 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 
        1963           24          489          476           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          19           26           45           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         405           10           30           14           39          323 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
          60          310          224           35          197          174 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK 
         218          297          127          377          476          121 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1965         1932          775           22          107          182 
TCGA-97-8174 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
        1965          148          197          271          392          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
          44          170          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 
         238          435          116         1967         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1980         1951         1944          142         1955         1490 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                  1 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              2696               2370 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             535.0              431.5 
[1] "2.0 - 2696.0 (535.0)" "1.0 - 2370.0 (431.5)"
[1] "hr=" "1.6"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  20Q GAIN MUTATED         4       43       52        17        30         23
  20Q GAIN WILD-TYPE       0       70       79        26        39         44
                    vv
clus                 STAGE IIIB STAGE IV
  20Q GAIN MUTATED            3        6
  20Q GAIN WILD-TYPE          8       17
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   4                  0
  STAGE IA                 43                 70
  STAGE IB                 52                 79
  STAGE IIA                17                 26
  STAGE IIB                30                 39
  STAGE IIIA               23                 44
  STAGE IIIB                3                  8
  STAGE IV                  6                 17
[1] 8 2
[1] 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    54 104  16   3
  20Q GAIN WILD-TYPE  89 155  24  15
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               54                 89
  T2              104                155
  T3               16                 24
  T4                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                  N0  N1 N2+N3
  20Q GAIN MUTATED   119  32    23
  20Q GAIN WILD-TYPE 176  53    49
D37V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                 119                176
  N1                  32                 53
  N2+N3               23                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  20Q GAIN MUTATED   115   5   0   1  55
  20Q GAIN WILD-TYPE 202  13   1   2  64
D37V6, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               115                202
  M1                 5                 13
  M1A                0                  1
  M1B                1                  2
  MX                55                 64
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    92  86
  20Q GAIN WILD-TYPE 156 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     92   86
  20Q GAIN WILD-TYPE  156  128
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               92                156
  MALE                 86                128
[1] 2 2
[1] FALSE
D37V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20Q GAIN MUTATED                            4
  20Q GAIN WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20Q GAIN MUTATED                                  28
  20Q GAIN WILD-TYPE                                65
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                  126
  20Q GAIN WILD-TYPE                                                168
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20Q GAIN MUTATED                                            1
  20Q GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20Q GAIN MUTATED                                               6
  20Q GAIN WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  20Q GAIN MUTATED                                0
  20Q GAIN WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  20Q GAIN MUTATED                                    2
  20Q GAIN WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  20Q GAIN MUTATED                              0                             7
  20Q GAIN WILD-TYPE                            2                            12
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  20Q GAIN MUTATED                                 0
  20Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  20Q GAIN MUTATED                                               3
  20Q GAIN WILD-TYPE                                             1
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  20Q GAIN MUTATED                              1
  20Q GAIN WILD-TYPE                            6
D37V9, multiclass
                                                    clus
vv                                                   20Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              126
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     7
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   20Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                168
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      12
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       1
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     5 173
  20Q GAIN WILD-TYPE  16 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5  173
  20Q GAIN WILD-TYPE   16  268
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 5                 16
  YES              173                268
[1] 2 2
[1] FALSE
D37V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   114   5   2   5
  20Q GAIN WILD-TYPE 204   6   2  14
D37V12, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              114                204
  R1                5                  6
  R2                2                  2
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  1     3
  20Q GAIN WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          14   136
  20Q GAIN WILD-TYPE                        12   226
D37V13, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                      14                 12
  WHITE                                         136                226
[1] 4 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     3 129
  20Q GAIN WILD-TYPE   4 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  129
  20Q GAIN WILD-TYPE    4  203
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              129                203
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    52  19
  21Q GAIN WILD-TYPE 269  63
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                71                332 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                 63 
$`21Q GAIN MUTATED`
TCGA-05-4405 TCGA-05-4415 TCGA-05-5423 TCGA-05-5428 TCGA-38-4628 TCGA-38-4629 
         610         1997          151          670         1492          864 
TCGA-38-6178 TCGA-44-2657 TCGA-44-2662 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 
         448          400         1280          845          658          705 
TCGA-44-6777 TCGA-44-A47A TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-49-6742 
        1942          466         1421          428          157          445 
TCGA-49-6743 TCGA-50-5049 TCGA-50-5931 TCGA-50-5941 TCGA-50-6597 TCGA-53-7626 
         369         2146          267          567         1015         1971 
TCGA-55-1595 TCGA-55-6642 TCGA-55-6980 TCGA-55-7727 TCGA-55-7914 TCGA-55-8206 
        1479          993           67           34            3           46 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8615 TCGA-55-A48Z TCGA-62-8398 TCGA-62-8399 
          66            9           15           29         1970         2696 
TCGA-64-1678 TCGA-64-1680 TCGA-67-3771 TCGA-67-6217 TCGA-69-8253 TCGA-69-A59K 
        1189         1126          610          422          100          214 
TCGA-71-6725 TCGA-73-4677 TCGA-73-7499 TCGA-75-6214 TCGA-78-7147 TCGA-78-7155 
          61           38          519         1970         1950         1957 
TCGA-78-7163 TCGA-78-7535 TCGA-78-7539 TCGA-78-7542 TCGA-78-8662 TCGA-86-8075 
        1950         1972          327         1952         1964          479 
TCGA-86-8279 TCGA-86-8358 TCGA-91-8496 TCGA-91-8499 TCGA-95-7944 TCGA-97-7546 
         482           19          197           36          377          964 
TCGA-97-7553 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-J2-A4AD TCGA-L9-A444 
        1332          147           15          115          287            6 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC 
         285          353         1954         1951         1944 

$`21Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
        1431          578         1958          455          912          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         913          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         730          457          882           30           62           14 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
         225          182          264         1952         1962         1147 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
        1073          354         1357         1971          133         1324 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1429         1367          741         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1130         1163         1036          190          722         1013 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
         863          383          723          328          302          704 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
        1938         1864         1978          444          592          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
         218          557         1970          882          535          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F 
         385           99          260          486          287          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 
         351          415           76         1932         1081          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
         268          896         1700          890          522          354 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2174          455          785          944         1499          246 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 
         282         1091         2370          653          883          764 
TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
         686          255          105         1986          424          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
         701         1178         1375           87            2           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        1239           25         1475         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1170           18           35          121            6            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
          95           40         1958           39           39           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 
          54           19           16          197           21           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33           21          100            6           43 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8299 
          26            4           47           15           33          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          44           23           29           11            8           15 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
         228            3          146          202          536           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
          49           66          106           33           42           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1952            1           28            5           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1216         1289         1445         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
         910         1728          628         1686         1968         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
          62         1305          864         1559          866           31 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
         573          427          385          174          141          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         186          690          414          165          230          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-73-4658 
          70           89          382           77          129         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
         711          912          800          467          131           40 
TCGA-73-4676 TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         164          621         1967         1956         1965         1973 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1988         1944         1093         1963         1202          760 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1948         1961         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
        1940         1934         1937         1965         1949         1944 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
         881          994         1949         1971         1981         1954 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1965         1972          824         1959           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         422         1968          591         1963          508          745 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
          10         1963           13           24          489          476 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
          16         1955           26           35           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          18           15          455          405           10           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          14           39          323         1940           60          310 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
          79          417          372          842          224           35 
TCGA-91-7771 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         492          174           44          218          297          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
         186           34            2          568          477          476 
TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
         121         1965         1932          775          181           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M2 
         107          182         1965           87          148          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         271          392          427          459           44          170 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         154          114          282          238          578          435 
TCGA-L9-A443 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         116          622         1946         1967         1951         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1957         1980         1970         1970          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                  1 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              2696               2370 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               482                456 
[1] "3.0 - 2696.0 (482.0)" "1.0 - 2370.0 (456.0)"
[1] "hr=" "1.1"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  21Q GAIN MUTATED         1       19       26        10         8         15
  21Q GAIN WILD-TYPE       3       94      105        33        61         52
                    vv
clus                 STAGE IIIB STAGE IV
  21Q GAIN MUTATED            3        3
  21Q GAIN WILD-TYPE          8       20
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 19                 94
  STAGE IB                 26                105
  STAGE IIA                10                 33
  STAGE IIB                 8                 61
  STAGE IIIA               15                 52
  STAGE IIIB                3                  8
  STAGE IV                  3                 20
[1] 8 2
[1] 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    28  49   6   2
  21Q GAIN WILD-TYPE 115 210  34  16
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               28                115
  T2               49                210
  T3                6                 34
  T4                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                  N0  N1 N2+N3
  21Q GAIN MUTATED    47  14    20
  21Q GAIN WILD-TYPE 248  71    52
D38V5, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                  47                248
  N1                  14                 71
  N2+N3               20                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  21Q GAIN MUTATED    59   3   0   0  22
  21Q GAIN WILD-TYPE 258  15   1   3  97
D38V6, multiclass
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                59                258
  M1                 3                 15
  M1A                0                  1
  M1B                0                  3
  MX                22                 97
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    53  32
  21Q GAIN WILD-TYPE 195 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     53   32
  21Q GAIN WILD-TYPE  195  182
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               53                195
  MALE                 32                182
[1] 2 2
[1] FALSE
D38V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  21Q GAIN MUTATED                            3
  21Q GAIN WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  21Q GAIN MUTATED                                  15
  21Q GAIN WILD-TYPE                                78
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                   56
  21Q GAIN WILD-TYPE                                                238
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  21Q GAIN MUTATED                                            0
  21Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  21Q GAIN MUTATED                                               4
  21Q GAIN WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  21Q GAIN MUTATED                                2
  21Q GAIN WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  21Q GAIN MUTATED                                    1
  21Q GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  21Q GAIN MUTATED                              0                             2
  21Q GAIN WILD-TYPE                            2                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  21Q GAIN MUTATED                                 0
  21Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  21Q GAIN MUTATED                                               1
  21Q GAIN WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  21Q GAIN MUTATED                              1
  21Q GAIN WILD-TYPE                            6
D38V9, multiclass
                                                    clus
vv                                                   21Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               56
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   21Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                238
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     4  81
  21Q GAIN WILD-TYPE  17 360
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4   81
  21Q GAIN WILD-TYPE   17  360
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 4                 17
  YES               81                360
[1] 2 2
[1] FALSE
D38V11, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    62   2   0   4
  21Q GAIN WILD-TYPE 256   9   4  15
D38V12, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               62                256
  R1                2                  9
  R2                0                  4
  RX                4                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     2
  21Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           5    66
  21Q GAIN WILD-TYPE                        21   296
D38V13, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       5                 21
  WHITE                                          66                296
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  60
  21Q GAIN WILD-TYPE   6 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   60
  21Q GAIN WILD-TYPE    6  272
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               60                272
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    35  13
  22Q GAIN WILD-TYPE 286  69
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                48                355 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                13                 69 
$`22Q GAIN MUTATED`
TCGA-05-4410 TCGA-05-4420 TCGA-38-4625 TCGA-38-A44F TCGA-44-3398 TCGA-44-6777 
        1958          912         1952          133         1163         1942 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7670 TCGA-44-A47A TCGA-44-A47F TCGA-49-6742 
        1978          218          882          466          337          445 
TCGA-49-6743 TCGA-50-5931 TCGA-50-5944 TCGA-55-1592 TCGA-55-1596 TCGA-55-6712 
         369          267          764          701         1375           24 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-8091 TCGA-55-8096 TCGA-55-8506 
        1958           39           16           43           47           11 
TCGA-55-8514 TCGA-55-8614 TCGA-55-A491 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
         202          536         1952         1289         1970         1445 
TCGA-67-3770 TCGA-67-3771 TCGA-73-4675 TCGA-78-7150 TCGA-78-7154 TCGA-78-8662 
          31          610           40         1963         1948         1964 
TCGA-86-7713 TCGA-86-8055 TCGA-86-8073 TCGA-86-8280 TCGA-91-6847 TCGA-95-7944 
         422           10           13           16          842          377 
TCGA-97-8174 TCGA-97-8552 TCGA-99-8033 TCGA-J2-A4AE TCGA-MP-A4SW TCGA-MP-A4T7 
        1965          115          170          282         1967         1954 

$`22Q GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
        1431          578          610         1997          455          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         913          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         730          457          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
          62           14          225          182          264         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1147         1492          864         1073          354         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
         448         1971         1324         1429          400         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         741         1280         1301           97          246         1130 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1036          190          722         1013          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         723          328          302          845          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
         705         1938         1864          444          592          366 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
         557         1970          535          719          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         260          486          287          351          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        1932         1081         1421          428          999          268 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
         896          157         1700          890          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        2174         2146          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         246          282         1091         2370          653          567 
TCGA-50-5942 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         883          686         1015          255          105         1986 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 
        1971          424          280         1178         1479           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
           2          993         1239           25         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1826         1233         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 
         121            6            4           95           40           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
          34           24           54           19          197           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
           3           31            5           33           21          100 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
           6           26            4           15           33           46 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
          66          216           44           23           29            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
          15          228            9            3          146           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
          48           49           66          106           33           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          29           48            1           28            5           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
         162         1216         2696         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
         910         1728          628         1189         1686         1126 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1968         1959           62         1305          864         1559 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         866          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
         230          184           70           89          382          100 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
          77          129          214           61         1600          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
         912          800          467          131          164           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         621          519         1970         1967         1956         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
        1973         1988         1950         1944         1093         1202 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
         760         1957         1961         1963         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
         215         1940         1950         1934         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1972         1949         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 
         994         1949         1971         1981         1954         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
        1972          824         1959           11          630         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8074 
         591         1963          508          745         1963           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 
         479          489          476          482         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          26           35           45           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
         455          405           10           30           14           39 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
         323         1940           60          310           79          417 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         372          224           35          492          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
          36           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
          34            2          568          477          476          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         964         1965         1932         1332          775          181 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
          22          107          182           87          147           15 
TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         148          197          271          392          427          459 
TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 
          44          154          114          287          238          578 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         435          116            6          285          622          353 
TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1946         1951         1954         1957         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1944         1970         1970          142         1955         1971 
TCGA-MP-A5C7 
        1490 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                10                  1 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1978               2696 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               501                459 
[1] "10.0 - 1978.0 (501.0)" "1.0 - 2696.0 (459.0)" 
[1] "hr=" "1.3"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  22Q GAIN MUTATED         1       10       19         9         9          9
  22Q GAIN WILD-TYPE       3      103      112        34        60         58
                    vv
clus                 STAGE IIIB STAGE IV
  22Q GAIN MUTATED            0        3
  22Q GAIN WILD-TYPE         11       20
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 10                103
  STAGE IB                 19                112
  STAGE IIA                 9                 34
  STAGE IIB                 9                 60
  STAGE IIIA                9                 58
  STAGE IIIB                0                 11
  STAGE IV                  3                 20
[1] 8 2
[1] 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    13  39   6   1
  22Q GAIN WILD-TYPE 130 220  34  17
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               13                130
  T2               39                220
  T3                6                 34
  T4                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                  N0  N1 N2+N3
  22Q GAIN MUTATED    35  15     8
  22Q GAIN WILD-TYPE 260  70    64
D39V5, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                  35                260
  N1                  15                 70
  N2+N3                8                 64
[1] 3 2
[1] 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 M1B  MX
  22Q GAIN MUTATED    37   3   0   0  20
  22Q GAIN WILD-TYPE 280  15   1   3  99
D39V6, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                37                280
  M1                 3                 15
  M1A                0                  1
  M1B                0                  3
  MX                20                 99
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    37  23
  22Q GAIN WILD-TYPE 211 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     37   23
  22Q GAIN WILD-TYPE  211  191
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               37                211
  MALE                 23                191
[1] 2 2
[1] FALSE
D39V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  22Q GAIN MUTATED                            1
  22Q GAIN WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  22Q GAIN MUTATED                                   7
  22Q GAIN WILD-TYPE                                86
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                   45
  22Q GAIN WILD-TYPE                                                249
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  22Q GAIN MUTATED                                            0
  22Q GAIN WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  22Q GAIN MUTATED                                               3
  22Q GAIN WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  22Q GAIN MUTATED                                1
  22Q GAIN WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  22Q GAIN MUTATED                                    1
  22Q GAIN WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  22Q GAIN MUTATED                              0                             1
  22Q GAIN WILD-TYPE                            2                            18
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  22Q GAIN MUTATED                                 0
  22Q GAIN WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  22Q GAIN MUTATED                                               0
  22Q GAIN WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  22Q GAIN MUTATED                              1
  22Q GAIN WILD-TYPE                            6
D39V9, multiclass
                                                    clus
vv                                                   22Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               45
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     1
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   22Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  86
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                249
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      18
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     1  59
  22Q GAIN WILD-TYPE  20 382
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   59
  22Q GAIN WILD-TYPE   20  382
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 1                 20
  YES               59                382
[1] 2 2
[1] FALSE
D39V11, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    43   0   1   2
  22Q GAIN WILD-TYPE 275  11   3  17
D39V12, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               43                275
  R1                0                 11
  R2                1                  3
  RX                2                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     1
  22Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           3    48
  22Q GAIN WILD-TYPE                        23   314
D39V13, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       3                 23
  WHITE                                          48                314
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  42
  22Q GAIN WILD-TYPE   6 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   42
  22Q GAIN WILD-TYPE    6  290
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               42                290
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    45  11
  XQ GAIN WILD-TYPE 276  71
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               56               347 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               11                71 
$`XQ GAIN MUTATED`
TCGA-05-4426 TCGA-05-5423 TCGA-35-5375 TCGA-44-2655 TCGA-44-2659 TCGA-44-5645 
         791          151          264         1324         1367          383 
TCGA-44-6778 TCGA-44-8117 TCGA-44-A47A TCGA-44-A4SU TCGA-49-6761 TCGA-50-5933 
        1864          385          466           76          354         2370 
TCGA-50-5941 TCGA-50-5946 TCGA-53-7626 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
         567          686         1971           87            2           24 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 
        1170           18           39           16          197           31 
TCGA-55-7995 TCGA-55-8094 TCGA-55-8096 TCGA-55-A494 TCGA-64-1676 TCGA-64-1680 
           5            4           47            5         1728         1126 
TCGA-64-5775 TCGA-67-6215 TCGA-69-7980 TCGA-71-6725 TCGA-73-4676 TCGA-73-4677 
          62          174          382           61          164           38 
TCGA-75-7025 TCGA-75-7031 TCGA-78-7149 TCGA-78-7154 TCGA-78-7155 TCGA-78-7163 
        1967         1965         1093         1948         1957         1950 
TCGA-78-7535 TCGA-78-7539 TCGA-78-8640 TCGA-86-8055 TCGA-86-8075 TCGA-86-8358 
        1972          327         1949           10          479           19 
TCGA-86-A4P7 TCGA-91-8499 TCGA-95-7043 TCGA-97-7554 TCGA-97-7937 TCGA-97-8179 
          14           36            2          775          181           15 
TCGA-MP-A4T4 TCGA-MP-A4TI 
        1954         1955 

$`XQ GAIN WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 
         912          365          913          669          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         761          730          457          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 
          62           14          225          182         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1147         1492          864         1073          354         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
         448         1971          133         1429          400          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
        1036          190          722         1013          863          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
        1938         1942         1978          444          592          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
         218          557         1970          882          535          719 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
          99          260          486          287          337          351 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
         415         1932         1081         1421          428          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         268          896          157         1700          445          369 
TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         890          522         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         944         1499          246          282          267         1091 
TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         653          883          764         1015          255          105 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
        1986          424          280          701         1178         1479 
TCGA-55-1596 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
        1375          993         1239           25         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        1826         1233         2151           35          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 
           4           95           40         1958           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 
          24           54           19           21            3           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 
          21          100            6           43           26           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          29           11            8           15          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
           3          146          202          536           15           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
          49           66          106           33           42           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
          48         1952            1           28           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U 
        1216         1289         1970         2696         1445         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        2199         1246          910          628         1189         1686 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1968         1959         1305          864         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 
          31          610          573          427          385          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
         230          184           70           89          100           77 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         129          214         1600          711          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 
         467          131           40          621          519         1970 
TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
        1956         1973         1988         1950         1944         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
        1202          760         1961         1963         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
         215         1940         1934         1937         1965         1949 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
        1944          881         1952          994         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
          11          630          422         1968          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
         508          745         1963           13           24          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 
         476          482           16         1955           26           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          45           34           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          10           30           39          323         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
         310           79          417          372          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
          35          492          197          174           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
         297          127          186           34          568          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         477          476          121          964         1965         1932 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        1332           22          107          182         1965           87 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
         147          148          115          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         427          459           44          170          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         287          282          238          578          435          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
           6          285          622          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1951         1954         1957         1980         1951         1944 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1970          142         1971         1490 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                 1 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             2370              2696 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            340.5             482.0 
[1] "2.0 - 2370.0 (340.5)" "1.0 - 2696.0 (482.0)"
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  XQ GAIN MUTATED         1       16       18         9         7          8
  XQ GAIN WILD-TYPE       3       97      113        34        62         59
                   vv
clus                STAGE IIIB STAGE IV
  XQ GAIN MUTATED            2        5
  XQ GAIN WILD-TYPE          9       18
D40V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                16                97
  STAGE IB                18               113
  STAGE IIA                9                34
  STAGE IIB                7                62
  STAGE IIIA               8                59
  STAGE IIIB               2                 9
  STAGE IV                 5                18
[1] 8 2
[1] 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    19  38   4   4
  XQ GAIN WILD-TYPE 124 221  36  14
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              19               124
  T2              38               221
  T3               4                36
  T4               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                 N0  N1 N2+N3
  XQ GAIN MUTATED    41  14    10
  XQ GAIN WILD-TYPE 254  71    62
D40V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0                 41               254
  N1                 14                71
  N2+N3              10                62
[1] 3 2
[1] 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 M1B  MX
  XQ GAIN MUTATED    43   4   0   1  17
  XQ GAIN WILD-TYPE 274  14   1   2 102
D40V6, multiclass
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               43               274
  M1                4                14
  M1A               0                 1
  M1B               1                 2
  MX               17               102
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    31  35
  XQ GAIN WILD-TYPE 217 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     31   35
  XQ GAIN WILD-TYPE  217  179
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              31               217
  MALE                35               179
[1] 2 2
[1] FALSE
D40V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XQ GAIN MUTATED                            1
  XQ GAIN WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XQ GAIN MUTATED                                   9
  XQ GAIN WILD-TYPE                                84
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                   51
  XQ GAIN WILD-TYPE                                                243
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  XQ GAIN MUTATED                                            1
  XQ GAIN WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  XQ GAIN MUTATED                                               0
  XQ GAIN WILD-TYPE                                            19
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  XQ GAIN MUTATED                                0
  XQ GAIN WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  XQ GAIN MUTATED                                    1
  XQ GAIN WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  XQ GAIN MUTATED                              0                             3
  XQ GAIN WILD-TYPE                            2                            16
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  XQ GAIN MUTATED                                 0
  XQ GAIN WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  XQ GAIN MUTATED                                               0
  XQ GAIN WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  XQ GAIN MUTATED                              0
  XQ GAIN WILD-TYPE                            7
D40V9, multiclass
                                                    clus
vv                                                   XQ GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              51
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    0
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   XQ GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               243
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     19
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     16
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  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     3  63
  XQ GAIN WILD-TYPE  18 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   63
  XQ GAIN WILD-TYPE   18  378
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                3                18
  YES              63               378
[1] 2 2
[1] FALSE
D40V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    46   1   1   2
  XQ GAIN WILD-TYPE 272  10   3  17
D40V12, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              46               272
  R1               1                10
  R2               1                 3
  RX               2                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     1
  XQ GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           3    51
  XQ GAIN WILD-TYPE                        23   311
D40V13, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      3                23
  WHITE                                         51               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"
D40V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  40
  XQ GAIN WILD-TYPE   7 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   40
  XQ GAIN WILD-TYPE    7  292
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              40               292
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    48  18
  1P LOSS WILD-TYPE 273  64
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               66               337 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               18                64 
$`1P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 
        1523         1126         1947         1431         1997          455 
TCGA-05-4422 TCGA-05-5420 TCGA-38-4628 TCGA-44-3918 TCGA-44-5643 TCGA-44-6144 
         365          457         1492         1036         1013          723 
TCGA-44-7660 TCGA-44-A47F TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-6745 
         592          337         1081          999          268          522 
TCGA-49-6761 TCGA-50-5051 TCGA-50-5935 TCGA-50-7109 TCGA-53-7626 TCGA-55-1596 
         354          455          653          255         1971         1375 
TCGA-55-6972 TCGA-55-6986 TCGA-55-7283 TCGA-55-8090 TCGA-55-8205 TCGA-55-8507 
        1475         2151           35            6           33            8 
TCGA-55-8508 TCGA-55-8615 TCGA-55-A48Y TCGA-55-A492 TCGA-62-8398 TCGA-62-8402 
          15           15           42            1         1970         1445 
TCGA-62-A46U TCGA-64-5774 TCGA-64-5778 TCGA-69-7761 TCGA-69-7973 TCGA-73-4659 
        2067         1959         1305          186          230          711 
TCGA-73-4666 TCGA-73-4675 TCGA-73-4677 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 
         800           40           38         1956         1988         1944 
TCGA-78-7149 TCGA-78-7153 TCGA-78-7159 TCGA-78-7160 TCGA-80-5608 TCGA-86-6851 
        1093          760         1221          678         1972         1959 
TCGA-86-7701 TCGA-86-8054 TCGA-86-8278 TCGA-86-8669 TCGA-91-8499 TCGA-95-7043 
          11          745          476           34           36            2 
TCGA-95-7567 TCGA-97-7554 TCGA-97-8172 TCGA-97-8174 TCGA-MP-A4T7 TCGA-MP-A4TE 
         568          775          182         1965         1954         1970 

$`1P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 
         607          426         1369          578          610         1958 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         912          913          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         761          730          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1962         1147          864         1073          354         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
         448         1971          133         1324         1429          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1367          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 
        1130         1163          190          722          863          383 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 
        1938         1942         1864         1978          444          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
         218          557         1970          882          535          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
         385           99          260          486          466          287 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 
         351          415           76         1932         1421          428 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
         896          157         1700          445          369          890 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2174         2146          785          944         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 TCGA-50-5942 
         282          267         1091         2370          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
         764          686         1015          105         1986          424 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
         280          701         1178         1479           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 
         993           24         1239           25           67         1826 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1233         1170           18          121            6            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
          95           40         1958           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          24           54           19           16          197           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
           3           31            5           33           21          100 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
          43           26            4           47           15           46 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          66          216           44           23           29           11 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z 
          48           49           66          106           33           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          48         1952           28            5           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1216         1289         2696         2199         1246          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        1728          628         1189         1686         1126         1968 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
          62          864         1559          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         573          427          385          174          141          422 
TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
         202          690          414          165          184           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          89          382          100           77          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
          61         1600          912          467          131          164 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 
         621          519         1970         1967         1965         1973 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1950         1963         1202         1948         1957         1961 
TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
        1963          215         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1965         1972         1949         1944          327          881 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
        1952          994         1949         1971         1981         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1964         1965          824          630          422         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
         591         1963          508           10         1963           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
          24          479          489          482           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
          19           26           35           45           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
         455          405           10           30           14           39 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
         323         1940           60          310           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         372          842          224           35          492          197 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
         174           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
          34          377          477          476          121          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
        1965         1932         1332          181           22          107 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
          87          147           15          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         271          392          427          459           44          170 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
         154          114          287          282          238          578 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         435          116            6          285          622          353 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1946         1967         1951         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1944         1970          142         1955         1971 
TCGA-MP-A5C7 
        1490 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                 2 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             2151              2696 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              734               427 
[1] "1.0 - 2151.0 (734.0)" "2.0 - 2696.0 (427.0)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  1P LOSS MUTATED         1       13       15         7        11         20
  1P LOSS WILD-TYPE       3      100      116        36        58         47
                   vv
clus                STAGE IIIB STAGE IV
  1P LOSS MUTATED            4        4
  1P LOSS WILD-TYPE          7       19
D41V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                13               100
  STAGE IB                15               116
  STAGE IIA                7                36
  STAGE IIB               11                58
  STAGE IIIA              20                47
  STAGE IIIB               4                 7
  STAGE IV                 4                19
[1] 8 2
[1] 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    16  45   8   5
  1P LOSS WILD-TYPE 127 214  32  13
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              16               127
  T2              45               214
  T3               8                32
  T4               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                 N0  N1 N2+N3
  1P LOSS MUTATED    37  17    20
  1P LOSS WILD-TYPE 258  68    52
D41V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                 37               258
  N1                 17                68
  N2+N3              20                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  1P LOSS MUTATED    59   4   0   0  12
  1P LOSS WILD-TYPE 258  14   1   3 107
D41V6, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               59               258
  M1                4                14
  M1A               0                 1
  M1B               0                 3
  MX               12               107
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    35  40
  1P LOSS WILD-TYPE 213 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     35   40
  1P LOSS WILD-TYPE  213  174
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              35               213
  MALE                40               174
[1] 2 2
[1] FALSE
D41V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1P LOSS MUTATED                            3
  1P LOSS WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1P LOSS MUTATED                                  19
  1P LOSS WILD-TYPE                                74
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                   43
  1P LOSS WILD-TYPE                                                251
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1P LOSS MUTATED                                            0
  1P LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  1P LOSS MUTATED                                               3
  1P LOSS WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  1P LOSS MUTATED                                0
  1P LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  1P LOSS MUTATED                                    0
  1P LOSS WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  1P LOSS MUTATED                              0                             4
  1P LOSS WILD-TYPE                            2                            15
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  1P LOSS MUTATED                                 1
  1P LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  1P LOSS MUTATED                                               0
  1P LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  1P LOSS MUTATED                              2
  1P LOSS WILD-TYPE                            5
D41V9, multiclass
                                                    clus
vv                                                   1P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              43
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   1P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               251
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     15
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  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     4  71
  1P LOSS WILD-TYPE  17 370
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4   71
  1P LOSS WILD-TYPE   17  370
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                4                17
  YES              71               370
[1] 2 2
[1] FALSE
D41V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    50   1   1   4
  1P LOSS WILD-TYPE 268  10   3  15
D41V12, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              50               268
  R1               1                10
  R2               1                 3
  RX               4                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           3    58
  1P LOSS WILD-TYPE                        23   304
D41V13, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      3                23
  WHITE                                         58               304
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  53
  1P LOSS WILD-TYPE   7 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   53
  1P LOSS WILD-TYPE    7  279
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              53               279
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    20   6
  1Q LOSS WILD-TYPE 301  76
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               26               377 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                76 
$`1Q LOSS MUTATED`
TCGA-05-4396 TCGA-05-4422 TCGA-05-4427 TCGA-44-5643 TCGA-44-7660 TCGA-49-4507 
        1947          365          791         1013          592          268 
TCGA-49-6745 TCGA-49-6761 TCGA-50-7109 TCGA-55-6986 TCGA-55-8090 TCGA-55-8205 
         522          354          255         2151            6           33 
TCGA-55-8507 TCGA-55-8620 TCGA-62-8402 TCGA-64-5774 TCGA-64-5778 TCGA-73-4666 
           8           66         1445         1959         1305          800 
TCGA-75-7027 TCGA-78-7146 TCGA-86-6851 TCGA-86-8278 TCGA-91-8499 TCGA-95-7043 
        1956         1988         1959          476           36            2 
TCGA-97-8174 TCGA-MP-A4TF 
        1965         1970 

$`1Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
        1523          607          426         1369         1126         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         913          669          791          761          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         457          151          882          670           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          14          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1147         1492          864         1073          354         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
         448         1971          133         1324         1429          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1367          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
        1130         1163         1036          190          722          863 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
         383          723          328          302          845          704 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
         658          705         1938         1942         1864         1978 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         444          366          218          557         1970          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         535          719          385           99          260          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         466          287          337          351          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
        1932         1081         1421          428          999          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-50-5045 
         157         1700          445          369          890         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2146          455          785          944         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         282          267         1091         2370          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 
         883          764          686         1015          105         1986 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
        1971          424          280          701         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
        1375           87            2          993           24         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 
          25         1475           67         1826         1233         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
          18           35          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          54           19           16          197           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 
          31            5           33           21          100           43 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 
          26            4           47           15           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
         216           44           23           29           11           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
          15           48           49          106           33           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          29           48         1952            1           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
          47          162         1216         1289         1970         2696 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
        2067         2199         1246          910         1728          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 
        1189         1686         1126         1968           62          864 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        1559          866           31          610          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         690          414          165          230          184           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          89          382          100           77          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
          61         1600          711          912          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 
          40          164           38          621          519         1970 
TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        1967         1965         1973         1950         1944         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1963         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1963         1221          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        1934         1937         1965         1972         1949         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
         327          881         1952          994         1949         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
        1981         1954         1964         1965         1972          824 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
          11          630          422         1968          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
         508          745           10         1963           13           24 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
         479          489          482           16         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          26           35           45           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
         455          405           10           30           14           39 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
         323         1940           60          310           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         372          842          224           35          492          197 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
         174           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
          34          568          377          477          476          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         964         1965         1932         1332          775          181 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
          22          107          182           87          147           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
         148          115          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         282          238          578          435          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         285          622          353         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1954         1954         1957         1980         1951         1944 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                 1 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             2151              2696 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            691.5             455.0 
[1] "2.0 - 2151.0 (691.5)" "1.0 - 2696.0 (455.0)"
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  1Q LOSS MUTATED         1        4        6         3         3          8
  1Q LOSS WILD-TYPE       3      109      125        40        66         59
                   vv
clus                STAGE IIIB STAGE IV
  1Q LOSS MUTATED            1        2
  1Q LOSS WILD-TYPE         10       21
D42V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 4               109
  STAGE IB                 6               125
  STAGE IIA                3                40
  STAGE IIB                3                66
  STAGE IIIA               8                59
  STAGE IIIB               1                10
  STAGE IV                 2                21
[1] 8 2
[1] 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     8  16   2   1
  1Q LOSS WILD-TYPE 135 243  38  17
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               8               135
  T2              16               243
  T3               2                38
  T4               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                 N0  N1 N2+N3
  1Q LOSS MUTATED    15   6     7
  1Q LOSS WILD-TYPE 280  79    65
D42V5, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0                 15               280
  N1                  6                79
  N2+N3               7                65
[1] 3 2
[1] 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 M1B  MX
  1Q LOSS MUTATED    20   1   0   1   6
  1Q LOSS WILD-TYPE 297  17   1   2 113
D42V6, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               20               297
  M1                1                17
  M1A               0                 1
  M1B               1                 2
  MX                6               113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    14  14
  1Q LOSS WILD-TYPE 234 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14   14
  1Q LOSS WILD-TYPE  234  200
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              14               234
  MALE                14               200
[1] 2 2
[1] FALSE
D42V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1Q LOSS MUTATED                            0
  1Q LOSS WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1Q LOSS MUTATED                                   7
  1Q LOSS WILD-TYPE                                86
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                   17
  1Q LOSS WILD-TYPE                                                277
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1Q LOSS MUTATED                                            0
  1Q LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  1Q LOSS MUTATED                                               2
  1Q LOSS WILD-TYPE                                            17
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  1Q LOSS MUTATED                                0
  1Q LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  1Q LOSS MUTATED                                    0
  1Q LOSS WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  1Q LOSS MUTATED                              0                             1
  1Q LOSS WILD-TYPE                            2                            18
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  1Q LOSS MUTATED                                 0
  1Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  1Q LOSS MUTATED                                               0
  1Q LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  1Q LOSS MUTATED                              1
  1Q LOSS WILD-TYPE                            6
D42V9, multiclass
                                                    clus
vv                                                   1Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              17
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   1Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 86
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               277
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     18
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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  25
  1Q LOSS WILD-TYPE  18 416
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   25
  1Q LOSS WILD-TYPE   18  416
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                3                18
  YES              25               416
[1] 2 2
[1] FALSE
D42V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    17   0   0   0
  1Q LOSS WILD-TYPE 301  11   4  19
D42V12, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              17               301
  R1               0                11
  R2               0                 4
  RX               0                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     0
  1Q LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           2    22
  1Q LOSS WILD-TYPE                        24   340
D42V13, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      2                24
  WHITE                                         22               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"
D42V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  21
  1Q LOSS WILD-TYPE   7 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   21
  1Q LOSS WILD-TYPE    7  311
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              21               311
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    18   3
  2P LOSS WILD-TYPE 303  79
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               21               382 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                79 
$`2P LOSS MUTATED`
TCGA-05-4410 TCGA-44-2665 TCGA-44-6778 TCGA-50-7109 TCGA-55-6986 TCGA-55-7726 
        1958         1301         1864          255         2151           39 
TCGA-55-8097 TCGA-62-8397 TCGA-62-A471 TCGA-64-1676 TCGA-67-3772 TCGA-71-6725 
          15         1289         1246         1728          573           61 
TCGA-73-7499 TCGA-78-7153 TCGA-78-7220 TCGA-86-8074 TCGA-97-7937 TCGA-97-8172 
         519          760         1965           24          181          182 
TCGA-97-8174 TCGA-L4-A4E5 TCGA-MP-A4T8 
        1965          578         1957 

$`2P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
        1431          578          610         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         365          913          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          730          457          151          882          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
          30           62           14          225          182          264 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        1952         1962         1147         1492          864         1073 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
         354         1357          448         1971          133         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2666 
        1429          400         1367          741         1280           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1013          863          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
        1978          444          592          366          218          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
        1970          882          535          719          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
         260          486          466          287          337          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         415           76         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         999          268          896          157         1700          445 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
         369          890          522          354         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         267         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         764          686         1015          105         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
         424          280          701         1178         1479         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
          87            2          993           24         1239           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
        1475           67         1826         1233         1170           18 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          35          121            6            4           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1958           39           34           24           54           19 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          16          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33           21          100            6           43           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
           4           47           33           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          44           23           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
          15           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          42           29           48         1952            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 
           5           47          162         1216         1970         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
        1445         2067         2199          910          628         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1686         1126         1968         1959           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 
         864         1559          866           31          610          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         690          414          165          230          184           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          89          382          100           77          129          214 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        1600          711          912          800          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-75-7025 
          40          164           38          621         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1956         1965         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1093         1963         1202         1948         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1963         1221          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1972         1949         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881         1952          994         1949         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
          11          630          422         1968          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
         508          745           10         1963           13          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
         489          476          482           16         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          26           35           45           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
         455          405           10           30           14           39 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
         323         1940           60          310           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         372          842          224           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         174           36           44          218          297          127 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         186           34            2          568          377          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         476          121          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
         775           22          107           87          147           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
         148          115          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         282          238          435          116            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         622          353         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1980         1951         1944         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15                 1 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2151              2696 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              760               455 
[1] "15.0 - 2151.0 (760.0)" "1.0 - 2696.0 (455.0)" 
[1] "hr=" "2"  
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  2P LOSS MUTATED         2        4        9         2         3          3
  2P LOSS WILD-TYPE       2      109      122        41        66         64
                   vv
clus                STAGE IIIB STAGE IV
  2P LOSS MUTATED            0        1
  2P LOSS WILD-TYPE         11       22
D43V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                 4               109
  STAGE IB                 9               122
  STAGE IIA                2                41
  STAGE IIB                3                66
  STAGE IIIA               3                64
  STAGE IIIB               0                11
  STAGE IV                 1                22
[1] 8 2
[1] 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     7  16   1   0
  2P LOSS WILD-TYPE 136 243  39  18
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               7               136
  T2              16               243
  T3               1                39
  T4               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                 N0  N1 N2+N3
  2P LOSS MUTATED    18   3     3
  2P LOSS WILD-TYPE 277  82    69
D43V5, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0                 18               277
  N1                  3                82
  N2+N3               3                69
[1] 3 2
[1] 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 M1B  MX
  2P LOSS MUTATED    18   1   0   0   5
  2P LOSS WILD-TYPE 299  17   1   3 114
D43V6, multiclass
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               18               299
  M1                1                17
  M1A               0                 1
  M1B               0                 3
  MX                5               114
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    15   9
  2P LOSS WILD-TYPE 233 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     15    9
  2P LOSS WILD-TYPE  233  205
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              15               233
  MALE                 9               205
[1] 2 2
[1] FALSE
D43V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2P LOSS MUTATED                            1
  2P LOSS WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2P LOSS MUTATED                                   5
  2P LOSS WILD-TYPE                                88
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                   13
  2P LOSS WILD-TYPE                                                281
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2P LOSS MUTATED                                            0
  2P LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  2P LOSS MUTATED                                               1
  2P LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  2P LOSS MUTATED                                0
  2P LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  2P LOSS MUTATED                                    1
  2P LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  2P LOSS MUTATED                              0                             2
  2P LOSS WILD-TYPE                            2                            17
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  2P LOSS MUTATED                                 0
  2P LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  2P LOSS MUTATED                                               0
  2P LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  2P LOSS MUTATED                              1
  2P LOSS WILD-TYPE                            6
D43V9, multiclass
                                                    clus
vv                                                   2P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                5
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              13
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   2P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 88
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     17
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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  23
  2P LOSS WILD-TYPE  20 418
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   23
  2P LOSS WILD-TYPE   20  418
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                1                20
  YES              23               418
[1] 2 2
[1] FALSE
D43V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    13   0   0   2
  2P LOSS WILD-TYPE 305  11   4  17
D43V12, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              13               305
  R1               0                11
  R2               0                 4
  RX               2                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     1
  2P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           1    19
  2P LOSS WILD-TYPE                        25   343
D43V13, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      1                25
  WHITE                                         19               343
[1] 4 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     0  17
  2P LOSS WILD-TYPE   7 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   17
  2P LOSS WILD-TYPE    7  315
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              17               315
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    17   1
  2Q LOSS WILD-TYPE 304  81
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               385 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                81 
$`2Q LOSS MUTATED`
TCGA-44-6778 TCGA-50-5946 TCGA-55-6986 TCGA-55-8097 TCGA-62-8397 TCGA-64-1676 
        1864          686         2151           15         1289         1728 
TCGA-67-3772 TCGA-69-7760 TCGA-71-6725 TCGA-73-7499 TCGA-78-7153 TCGA-86-8054 
         573          202           61          519          760          745 
TCGA-86-8074 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-L4-A4E5 TCGA-MP-A4T8 
          24          775          181          182          578         1957 

$`2Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
         761          761          730          457          151          882 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
         670           30           62           14          225          182 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
         264         1952         1962         1147         1492          864 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
        1073          354         1357          448         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
        1324         1429          400         1367          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
         190          722         1013          863          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
        1938         1942         1978          444          592          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
         218          557         1970          882          535          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
         385           99          260          486          466          287 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         337          351          415           76         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        1700          445          369          890          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        2174         2146          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         246          282          267         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         567          883          764         1015          255          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
        1986         1971          424          280          701         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        1479         1375           87            2          993           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
        1239           25         1475           67         1826         1233 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1170           18           35          121            6            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
          95           40         1958           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          24           54           19           16          197           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
           3           31            5           33           21          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 
           6           43           26            4           47           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          46           66          216           44           23           29 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          11            8           15          228            9            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
         146          202          536           15           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          66          106           33           42           29           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1952            1           28            5           47          162 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
        1216         1970         2696         1445         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
        1246          910          628         1189         1686         1126 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1968         1959           62         1305          864         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
         866           31          610          427          385          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         141          422          186          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
         230          184           70           89          382          100 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
          77          129          214         1600          711          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
         800          467          131           40          164           38 
TCGA-73-7498 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         621         1970         1967         1956         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1988         1950         1944         1093         1963         1202 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
        1948         1957         1961         1963         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
         215         1940         1950         1934         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1972         1949         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         994         1949         1971         1981         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1965         1972          824         1959           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
         422         1968          591         1963          508           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        1963           13          479          489          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
          16         1955           19           26           35           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          34           18           15          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          30           14           39          323         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
         310           79          417          372          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          35          492          197          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         218          297          127          186           34            2 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
         568          377          477          476          121          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
        1965         1932         1332           22          107         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
          87          147           15          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         271          392          427          459           44          170 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
         154          114          287          282          238          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         116            6          285          622          353         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1967         1951         1954         1954         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1944         1970         1970          142         1955         1971 
TCGA-MP-A5C7 
        1490 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15                 1 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2151              2696 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              632               455 
[1] "15.0 - 2151.0 (632.0)" "1.0 - 2696.0 (455.0)" 
[1] "hr=" "3.7"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  2Q LOSS MUTATED         1        4        9         1         4          3
  2Q LOSS WILD-TYPE       3      109      122        42        65         64
                   vv
clus                STAGE IIIB STAGE IV
  2Q LOSS MUTATED            0        1
  2Q LOSS WILD-TYPE         11       22
D44V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                 4               109
  STAGE IB                 9               122
  STAGE IIA                1                42
  STAGE IIB                4                65
  STAGE IIIA               3                64
  STAGE IIIB               0                11
  STAGE IV                 1                22
[1] 8 2
[1] 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     6  15   2   0
  2Q LOSS WILD-TYPE 137 244  38  18
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               6               137
  T2              15               244
  T3               2                38
  T4               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                 N0  N1 N2+N3
  2Q LOSS MUTATED    17   3     3
  2Q LOSS WILD-TYPE 278  82    69
D44V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0                 17               278
  N1                  3                82
  N2+N3               3                69
[1] 3 2
[1] 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 M1B  MX
  2Q LOSS MUTATED    18   1   0   0   4
  2Q LOSS WILD-TYPE 299  17   1   3 115
D44V6, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               18               299
  M1                1                17
  M1A               0                 1
  M1B               0                 3
  MX                4               115
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    14   9
  2Q LOSS WILD-TYPE 234 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     14    9
  2Q LOSS WILD-TYPE  234  205
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              14               234
  MALE                 9               205
[1] 2 2
[1] FALSE
D44V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2Q LOSS MUTATED                            3
  2Q LOSS WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2Q LOSS MUTATED                                   4
  2Q LOSS WILD-TYPE                                89
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                   11
  2Q LOSS WILD-TYPE                                                283
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2Q LOSS MUTATED                                            0
  2Q LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  2Q LOSS MUTATED                                               1
  2Q LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  2Q LOSS MUTATED                                0
  2Q LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  2Q LOSS MUTATED                                    1
  2Q LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  2Q LOSS MUTATED                              0                             2
  2Q LOSS WILD-TYPE                            2                            17
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  2Q LOSS MUTATED                                 0
  2Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  2Q LOSS MUTATED                                               0
  2Q LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  2Q LOSS MUTATED                              1
  2Q LOSS WILD-TYPE                            6
D44V9, multiclass
                                                    clus
vv                                                   2Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              11
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   2Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               283
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     17
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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     0  23
  2Q LOSS WILD-TYPE  21 418
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   23
  2Q LOSS WILD-TYPE   21  418
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                0                21
  YES              23               418
[1] 2 2
[1] FALSE
D44V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    13   0   0   1
  2Q LOSS WILD-TYPE 305  11   4  18
D44V12, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              13               305
  R1               0                11
  R2               0                 4
  RX               1                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     1
  2Q LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           1    17
  2Q LOSS WILD-TYPE                        25   345
D44V13, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      1                25
  WHITE                                         17               345
[1] 4 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  15
  2Q LOSS WILD-TYPE   7 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   15
  2Q LOSS WILD-TYPE    7  317
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              15               317
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   133  32
  3P LOSS WILD-TYPE 188  50
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              165               238 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               32                50 
$`3P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4432 
        1523          607         1369         1126         1997          761 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5715 TCGA-35-4122 TCGA-38-4627 TCGA-38-4628 
         457          882           62          225         1147         1492 
TCGA-38-6178 TCGA-44-2657 TCGA-44-2668 TCGA-44-5643 TCGA-44-6144 TCGA-44-6145 
         448          400          246         1013          723          328 
TCGA-44-6147 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
         845          658         1938         1864         1978          592 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         882          535          719          385           99          260 
TCGA-44-A479 TCGA-44-A47F TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
         486          337         1421          428          999          896 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-50-5049 TCGA-50-5068 TCGA-50-5072 
        1700          445          890         2146         1499          246 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-6597 TCGA-53-7624 
         267         1091          653          567         1015         1986 
TCGA-53-7626 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6983 TCGA-55-6985 
        1971         1178         1479         1375         1826         1233 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 
          35            6            4           40         1958           39 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-8090 TCGA-55-8094 
          34           16          197            3            6            4 
TCGA-55-8206 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 
          46           11            8           15          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
          15           48           66           29         1952            1 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A471 
          47          162         1289         1970         2696         1246 
TCGA-64-1676 TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1728         1189         1959          864         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 
          31          610          573          422          690          414 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 TCGA-73-4659 
         165          230           89          100           61          711 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 
         912          800          131           40          621          519 
TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7159 
        1970         1956         1965         1988         1944         1221 
TCGA-78-7160 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
         678         1937         1965         1972         1949          327 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1952         1949         1954         1972          824         1959 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7954 TCGA-86-8054 TCGA-86-8073 TCGA-86-8278 
          11          422         1963          745           13          476 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6829 
          16           19           35           34           30         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 
          60          310           79          842          492           36 
TCGA-91-A4BC TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 
          44          127           34            2          568          477 
TCGA-95-7948 TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 
         476          964          775          181         1965          147 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-MP-A4T8 
         271          154          114          238          578         1957 
TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI 
        1944         1970         1955 

$`3P LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 
         426         1947         1431          578          610         1958 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
         455          912          365          913          669          791 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
         791          761          730          151          670           30 
TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 
          14          182          264         1952         1962          864 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
        1073          354         1357         1971          133         1324 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
        1429         1367          741         1280         1301           97 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
        1130         1163         1036          190          722          863 
TCGA-44-5645 TCGA-44-6146 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 
         383          302          704          705         1942          444 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B 
         366          218          557         1970          466          287 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4507 
         351          415           76         1932         1081          268 
TCGA-49-4512 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 
         157          369          522          354         2174          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5933 TCGA-50-5942 TCGA-50-5944 
         785          944          282         2370          883          764 
TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         686          255          105          424          280          701 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
          87            2          993           24         1239           25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 
        1475           67         2151         1170           18          121 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
          95           39           24           54           19           21 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 
          31            5           33           21          100           43 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8299 
          26           47           15           33           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          44           23           29          228            9            3 
TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
         146           49          106           33           42           48 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
          28            5         1216         1445         2067         2199 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
         910          628         1686         1126         1968           62 
TCGA-64-5778 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
        1305          427          385          174          141          202 
TCGA-69-7761 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 
         186          184           70          382           77          129 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-75-7025 
         214         1600          467          164           38         1967 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1973         1950         1093         1963         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 
        1948         1957         1961         1963          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 
        1950         1934         1944          881          994         1971 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
        1981         1964         1965          630         1968          591 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
         508           10         1963           24          479          489 
TCGA-86-8279 TCGA-86-8281 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
         482         1955           26           45           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         455          405           10           14           39          323 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
         417          372          224           35          197          174 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7944 TCGA-95-A4VK TCGA-97-7547 
         218          297          186          377          121         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
        1932         1332           22          107          182           87 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 
          15          148          115          197          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 
         459           44          170          287          282          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         116            6          285          622          353         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1967         1951         1954         1954         1980         1951 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1971         1490 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                 2 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             2696              2370 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              578               416 
[1] "1.0 - 2696.0 (578.0)" "2.0 - 2370.0 (416.0)"
[1] "hr=" "1.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  3P LOSS MUTATED         1       43       50        23        31         30
  3P LOSS WILD-TYPE       3       70       81        20        38         37
                   vv
clus                STAGE IIIB STAGE IV
  3P LOSS MUTATED            3       12
  3P LOSS WILD-TYPE          8       11
D45V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                43                70
  STAGE IB                50                81
  STAGE IIA               23                20
  STAGE IIB               31                38
  STAGE IIIA              30                37
  STAGE IIIB               3                 8
  STAGE IV                12                11
[1] 8 2
[1] 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    59 118  11   4
  3P LOSS WILD-TYPE  84 141  29  14
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              59                84
  T2             118               141
  T3              11                29
  T4               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                 N0  N1 N2+N3
  3P LOSS MUTATED   116  40    33
  3P LOSS WILD-TYPE 179  45    39
D45V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                116               179
  N1                 40                45
  N2+N3              33                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  3P LOSS MUTATED   134   9   0   2  47
  3P LOSS WILD-TYPE 183   9   1   1  72
D45V6, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              134               183
  M1                9                 9
  M1A               0                 1
  M1B               2                 1
  MX               47                72
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   103  90
  3P LOSS WILD-TYPE 145 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    103   90
  3P LOSS WILD-TYPE  145  124
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             103               145
  MALE                90               124
[1] 2 2
[1] FALSE
D45V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3P LOSS MUTATED                            5
  3P LOSS WILD-TYPE                          8
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3P LOSS MUTATED                                  44
  3P LOSS WILD-TYPE                                49
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                  124
  3P LOSS WILD-TYPE                                                170
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3P LOSS MUTATED                                            0
  3P LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  3P LOSS MUTATED                                               6
  3P LOSS WILD-TYPE                                            13
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  3P LOSS MUTATED                                1
  3P LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  3P LOSS MUTATED                                    1
  3P LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  3P LOSS MUTATED                              0                             6
  3P LOSS WILD-TYPE                            2                            13
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  3P LOSS MUTATED                                 1
  3P LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  3P LOSS MUTATED                                               1
  3P LOSS WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  3P LOSS MUTATED                              4
  3P LOSS WILD-TYPE                            3
D45V9, multiclass
                                                    clus
vv                                                   3P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               44
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             124
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    6
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    6
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     4
                                                    clus
vv                                                   3P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               170
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     13
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     13
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       3
[1] 12  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     9 184
  3P LOSS WILD-TYPE  12 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      9  184
  3P LOSS WILD-TYPE   12  257
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                9                12
  YES             184               257
[1] 2 2
[1] FALSE
D45V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED   132   2   1   4
  3P LOSS WILD-TYPE 186   9   3  15
D45V12, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0             132               186
  R1               2                 9
  R2               1                 3
  RX               4                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     3
  3P LOSS WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          15   152
  3P LOSS WILD-TYPE                        11   210
D45V13, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 3
  BLACK OR AFRICAN AMERICAN                     15                11
  WHITE                                        152               210
[1] 4 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     2 148
  3P LOSS WILD-TYPE   5 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2  148
  3P LOSS WILD-TYPE    5  184
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             148               184
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    94  19
  3Q LOSS WILD-TYPE 227  63
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              113               290 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19                63 
$`3Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4415 TCGA-05-4432 TCGA-05-5420 TCGA-05-5715 
        1523         1126         1997          761          457           62 
TCGA-35-4122 TCGA-38-4628 TCGA-44-6144 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 
         225         1492          723          658         1938         1864 
TCGA-44-6779 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
        1978          535          719          385           99          260 
TCGA-44-A479 TCGA-44-A47F TCGA-49-4506 TCGA-49-4510 TCGA-49-6742 TCGA-50-5068 
         486          337          999          896          445         1499 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
        1091          653         1015         1479         1375           87 
TCGA-55-6712 TCGA-55-6983 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7727 
          24         1826           35            4           40           34 
TCGA-55-7907 TCGA-55-7910 TCGA-55-8090 TCGA-55-8094 TCGA-55-8206 TCGA-55-8508 
          16          197            6            4           46           15 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A492 
         202           15           48           66           29            1 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-64-1676 
          47          162         1289         1970         2696         1728 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 
        1189         1959          864         1559           31          610 
TCGA-67-3772 TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
         573          422          690          414          165          184 
TCGA-69-8253 TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4675 
         100           61          711          912          800           40 
TCGA-73-7498 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7148 TCGA-78-7160 
         621         1970         1956         1965         1944          678 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7539 TCGA-78-8660 TCGA-80-5608 
        1937         1965         1972          327         1954         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7713 TCGA-86-7954 TCGA-86-8054 TCGA-86-8073 
         824         1959          422         1963          745           13 
TCGA-86-8280 TCGA-86-8585 TCGA-86-A4D0 TCGA-91-6847 TCGA-91-7771 TCGA-93-7348 
          16           35           30          842          492          127 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7554 
          34          568          476          121          964          775 
TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-J2-8192 TCGA-J2-8194 
         181          182         1965          147          154          114 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TI 
         238          578         1957         1944         1955 

$`3Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         607          426         1369         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
         610         1958          455          912          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 
         669          791          791          761          730          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 
         882          670           30           14          182          264 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1952         1962         1147          864         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1357          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
        1013          863          383          328          302          845 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
         704          705         1942          444          592          366 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-A47A TCGA-44-A47B 
         218          557         1970          882          466          287 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         351          415           76         1932         1081         1421 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
         428          268          157         1700          369          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         522          354         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 
         944          246          282          267         2370          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         883          764          686          255          105         1986 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-6543 
        1971          424          280          701         1178            2 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 
         993         1239           25         1475           67         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 
        2151         1170           18          121            6           95 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1958           39           39           24           54           19 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          21            3           31            5           33           21 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
         100           43           26           47           15           33 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          66          216           44           23           29           11 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
           8          228            9            3          146          536 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 
          49          106           33           42           48         1952 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
          28            5         1216         1445         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        1246          910          628         1686         1126         1968 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
          62         1305          866          427          385          174 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
         141          202          186          230           70           89 
TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4668 
         382           77          129          214         1600          467 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-7025 TCGA-78-7145 
         131          164           38          519         1967         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1988         1950         1093         1963         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 
        1948         1957         1961         1963         1221          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
        1940         1950         1934         1949         1944          881 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
        1952          994         1949         1971         1981         1964 
TCGA-80-5607 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
        1965           11          630         1968          591          508 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
          10         1963           24          479          489          476 
TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 
         482         1955           19           26           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
          18           15          455          405           10           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323         1940           60          310           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
         417          372          224           35          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7043 
          36           44          218          297          186            2 
TCGA-95-7944 TCGA-95-7947 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         377          477         1965         1932         1332           22 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
         107           87           15          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         271          392          427          459           44          170 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         287          282          435          116            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         622          353         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1954         1980         1951         1970         1970          142 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                 2 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             2696              2370 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              573               446 
[1] "1.0 - 2696.0 (573.0)" "2.0 - 2370.0 (446.0)"
[1] "hr=" "1.3"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  3Q LOSS MUTATED         1       28       31        15        24         24
  3Q LOSS WILD-TYPE       3       85      100        28        45         43
                   vv
clus                STAGE IIIB STAGE IV
  3Q LOSS MUTATED            3        7
  3Q LOSS WILD-TYPE          8       16
D46V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                28                85
  STAGE IB                31               100
  STAGE IIA               15                28
  STAGE IIB               24                45
  STAGE IIIA              24                43
  STAGE IIIB               3                 8
  STAGE IV                 7                16
[1] 8 2
[1] 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    39  81   9   4
  3Q LOSS WILD-TYPE 104 178  31  14
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              39               104
  T2              81               178
  T3               9                31
  T4               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                 N0  N1 N2+N3
  3Q LOSS MUTATED    76  30    27
  3Q LOSS WILD-TYPE 219  55    45
D46V5, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0                 76               219
  N1                 30                55
  N2+N3              27                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  3Q LOSS MUTATED    97   4   0   2  30
  3Q LOSS WILD-TYPE 220  14   1   1  89
D46V6, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               97               220
  M1                4                14
  M1A               0                 1
  M1B               2                 1
  MX               30                89
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    70  63
  3Q LOSS WILD-TYPE 178 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     70   63
  3Q LOSS WILD-TYPE  178  151
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              70               178
  MALE                63               151
[1] 2 2
[1] FALSE
D46V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3Q LOSS MUTATED                            5
  3Q LOSS WILD-TYPE                          8
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3Q LOSS MUTATED                                  32
  3Q LOSS WILD-TYPE                                61
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                   78
  3Q LOSS WILD-TYPE                                                216
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3Q LOSS MUTATED                                            0
  3Q LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  3Q LOSS MUTATED                                               5
  3Q LOSS WILD-TYPE                                            14
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  3Q LOSS MUTATED                                1
  3Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  3Q LOSS MUTATED                                    1
  3Q LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  3Q LOSS MUTATED                              0                             5
  3Q LOSS WILD-TYPE                            2                            14
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  3Q LOSS MUTATED                                 1
  3Q LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  3Q LOSS MUTATED                                               1
  3Q LOSS WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  3Q LOSS MUTATED                              4
  3Q LOSS WILD-TYPE                            3
D46V9, multiclass
                                                    clus
vv                                                   3Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              78
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    5
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    5
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     4
                                                    clus
vv                                                   3Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               216
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     14
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     14
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       3
[1] 12  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     6 127
  3Q LOSS WILD-TYPE  15 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6  127
  3Q LOSS WILD-TYPE   15  314
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                6                15
  YES             127               314
[1] 2 2
[1] FALSE
D46V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    87   1   0   5
  3Q LOSS WILD-TYPE 231  10   4  14
D46V12, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              87               231
  R1               1                10
  R2               0                 4
  RX               5                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     3
  3Q LOSS WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                          13   101
  3Q LOSS WILD-TYPE                        13   261
D46V13, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 3
  BLACK OR AFRICAN AMERICAN                     13                13
  WHITE                                        101               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"
D46V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0 104
  3Q LOSS WILD-TYPE   7 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0  104
  3Q LOSS WILD-TYPE    7  228
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO             104               228
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    79  12
  4P LOSS WILD-TYPE 242  70
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               91               312 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               12                70 
$`4P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 
        1523         1431          610         1958         1997          912 
TCGA-05-4424 TCGA-05-5420 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-44-2659 
         913          457          182          264         1952         1367 
TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1036         1013          863          723          328          302 
TCGA-44-6147 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-8117 TCGA-44-A479 
         845         1864          592          557          385          486 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-6742 TCGA-49-6743 TCGA-50-5049 
        1421          999          268          445          369         2146 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5946 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1596 
         455          944          686         1971          280         1375 
TCGA-55-6971 TCGA-55-6985 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 
          25         1233           95           40         1958           39 
TCGA-55-7815 TCGA-55-7910 TCGA-55-8505 TCGA-55-8507 TCGA-55-8514 TCGA-55-8614 
          54          197           29            8          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A4DF TCGA-55-A4DG 
          15           48           29         1952           47          162 
TCGA-62-8398 TCGA-62-A46U TCGA-62-A472 TCGA-64-1677 TCGA-64-5778 TCGA-64-5779 
        1970         2067          910          628         1305          864 
TCGA-64-5815 TCGA-67-3771 TCGA-69-7763 TCGA-69-7973 TCGA-69-7979 TCGA-69-A59K 
         866          610          690          230           89          214 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-78-7159 TCGA-78-7536 
          61          711          131           40         1221         1949 
TCGA-78-8640 TCGA-86-7713 TCGA-86-7954 TCGA-86-8055 TCGA-86-8075 TCGA-86-8358 
        1949          422         1963           10          479           19 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-95-7043 
        1940           60          310          372          842            2 
TCGA-95-7567 TCGA-95-7944 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 
         568          377          427          170          287          578 
TCGA-MN-A4N4 
         622 

$`4P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 
         607          426         1369         1126         1947          578 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         455          365          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         761          730          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
          62           14          225         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         864         1073          354         1357          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
         133         1324         1429          400          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
        1301           97          246         1130         1163          190 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         722          383          704          658          705         1938 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
        1942         1978          444          366          218         1970 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A 
         882          535          719           99          260          466 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         287          337          351          415           76         1932 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 
        1081          428          896          157         1700          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 
         522          354         2174          785         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         282          267         1091         2370          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         883          764         1015          255          105         1986 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
         424          701         1178         1479           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
         993           24         1239         1475           67         1826 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        2151         1170           18           35          121            6 
TCGA-55-7573 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 
           4           39           34           24           19           16 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          21            3           31            5           33           21 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
         100            6           43           26            4           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
          15           33           46           66          216           44 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          23           11           15          228            9            3 
TCGA-55-8513 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         146           49           66          106           33           42 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 
          48            1           28            5         1216         1289 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 
        2696         1445         2199         1246         1728         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 
        1686         1126         1968         1959           62         1559 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
          31          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
         422          202          186          414          165          184 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-73-4658 
          70          382          100           77          129         1600 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         912          800          467          164           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         519         1970         1967         1956         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1988         1950         1944         1093         1963         1202 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
         760         1948         1957         1961         1963          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
         215         1940         1950         1934         1937         1965 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1972         1944          327          881         1952          994 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1971         1981         1954         1964         1965         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
         824         1959           11          630         1968          591 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
         508          745         1963           13           24          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 
         476          482           16         1955           26           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          45           34           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6835 
          10           30           14           39          323           79 
TCGA-91-6836 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         417          224           35          492          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
          36           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
          34          477          476          121          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
        1932         1332          775          181           22          107 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
         182         1965           87          147           15          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
         115          197          271          392          459           44 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
         154          114          282          238          435          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
           6          285          353         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1954         1954         1957         1980         1951         1944 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1970          142         1955         1971         1490 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                 1 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2146              2696 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            557.0             451.5 
[1] "2.0 - 2146.0 (557.0)" "1.0 - 2696.0 (451.5)"
[1] "hr=" "1.4"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  4P LOSS MUTATED         1       24       34         7        14         17
  4P LOSS WILD-TYPE       3       89       97        36        55         50
                   vv
clus                STAGE IIIB STAGE IV
  4P LOSS MUTATED            5        5
  4P LOSS WILD-TYPE          6       18
D47V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                24                89
  STAGE IB                34                97
  STAGE IIA                7                36
  STAGE IIB               14                55
  STAGE IIIA              17                50
  STAGE IIIB               5                 6
  STAGE IV                 5                18
[1] 8 2
[1] 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    31  60  10   4
  4P LOSS WILD-TYPE 112 199  30  14
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              31               112
  T2              60               199
  T3              10                30
  T4               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                 N0  N1 N2+N3
  4P LOSS MUTATED    67  15    21
  4P LOSS WILD-TYPE 228  70    51
D47V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                 67               228
  N1                 15                70
  N2+N3              21                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  4P LOSS MUTATED    72   5   0   0  29
  4P LOSS WILD-TYPE 245  13   1   3  90
D47V6, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               72               245
  M1                5                13
  M1A               0                 1
  M1B               0                 3
  MX               29                90
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    54  53
  4P LOSS WILD-TYPE 194 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     54   53
  4P LOSS WILD-TYPE  194  161
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              54               194
  MALE                53               161
[1] 2 2
[1] FALSE
D47V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4P LOSS MUTATED                            3
  4P LOSS WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4P LOSS MUTATED                                  22
  4P LOSS WILD-TYPE                                71
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                   72
  4P LOSS WILD-TYPE                                                222
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4P LOSS MUTATED                                            0
  4P LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  4P LOSS MUTATED                                               3
  4P LOSS WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  4P LOSS MUTATED                                1
  4P LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  4P LOSS MUTATED                                    0
  4P LOSS WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  4P LOSS MUTATED                              1                             1
  4P LOSS WILD-TYPE                            1                            18
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  4P LOSS MUTATED                                 1
  4P LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  4P LOSS MUTATED                                               1
  4P LOSS WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  4P LOSS MUTATED                              2
  4P LOSS WILD-TYPE                            5
D47V9, multiclass
                                                    clus
vv                                                   4P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              72
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                    1
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   4P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               222
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     18
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  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     6 101
  4P LOSS WILD-TYPE  15 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6  101
  4P LOSS WILD-TYPE   15  340
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                6                15
  YES             101               340
[1] 2 2
[1] FALSE
D47V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED    71   3   1   8
  4P LOSS WILD-TYPE 247   8   3  11
D47V12, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              71               247
  R1               3                 8
  R2               1                 3
  RX               8                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          10    78
  4P LOSS WILD-TYPE                        16   284
D47V13, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                     10                16
  WHITE                                         78               284
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  80
  4P LOSS WILD-TYPE   6 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   80
  4P LOSS WILD-TYPE    6  252
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              80               252
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    87  17
  4Q LOSS WILD-TYPE 234  65
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              104               299 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               17                65 
$`4Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4398 TCGA-05-4405 TCGA-05-4415 TCGA-05-4420 
        1523          607         1431          610         1997          912 
TCGA-05-4424 TCGA-05-5420 TCGA-35-4123 TCGA-35-5375 TCGA-38-6178 TCGA-44-5643 
         913          457          182          264          448         1013 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6778 TCGA-44-7660 
         863          723          328          845         1864          592 
TCGA-44-7667 TCGA-44-A479 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-6743 
         557          486         1421          999          268          369 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5946 TCGA-50-7109 TCGA-53-A4EZ 
        2146          455          944          686          255          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6971 TCGA-55-7573 TCGA-55-7574 
         701         1178         1375           25            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7815 TCGA-55-7910 TCGA-55-8092 
          40         1958           39           54          197           26 
TCGA-55-8094 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8616 
           4           29            8           15          202           48 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-62-8398 
          42           29         1952            1           47         1970 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 
        2067          910          628         1686         1968         1305 
TCGA-64-5779 TCGA-67-3771 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7979 
         864          610          690          414          230           89 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 
         129           61          711          912          131           40 
TCGA-75-6214 TCGA-75-7031 TCGA-78-7159 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
        1970         1965         1221         1937         1972         1949 
TCGA-78-8640 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8075 
        1949          422         1963          508           10          479 
TCGA-86-8279 TCGA-86-8669 TCGA-86-8672 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
         482           34           15         1940           60          310 
TCGA-91-6840 TCGA-91-6847 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-97-7937 
         372          842            2          568          377          181 
TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-MN-A4N4 
         427           44          170          287          578          622 
TCGA-MP-A4TA TCGA-MP-A4TF 
        1951         1970 

$`4Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 
         426         1369         1126         1947          578         1958 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         455          365          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         761          730          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
          62           14          225         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 
        1492          864         1073          354         1357         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6146 TCGA-44-6148 
        1036          190          722          383          302          704 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
         658          705         1938         1942         1978          444 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
         366          218         1970          882          535          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
         385           99          260          466          287          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 
         351          415           76         1932         1081          428 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
         896          157         1700          445          890          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         354         2174          785         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         267         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
         764         1015          105         1986         1971          424 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
        1479           87            2          993           24         1239 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        1475           67         1826         1233         2151         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7725 TCGA-55-7727 
          18           35          121            6           39           34 
TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          24           19           16           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33           21          100            6           43 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
          47           15           33           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          44           23           11          228            9            3 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         146          536           15           49           66          106 
TCGA-55-A48X TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 
          33           48           28            5          162         1216 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 
        1289         2696         1445         2199         1246         1728 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 
        1189         1126         1959           62         1559          866 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
          31          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
         422          202          186          165          184           70 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 TCGA-73-4666 
         382          100           77          214         1600          800 
TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 
         467          164           38          621          519         1967 
TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        1956         1973         1988         1950         1944         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1963         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1963          678          215         1940         1950         1934 
TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1965         1944          327          881         1952          994 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1971         1981         1954         1964         1965         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
         824         1959           11          630         1968          591 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
         745         1963           13           24          489          476 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
          16         1955           19           26           35           45 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          18          455          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-91-6848 TCGA-91-6849 
          39          323           79          417          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          197          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7947 TCGA-95-7948 
         297          127          186           34          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         121          964         1965         1932         1332          775 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
          22          107          182         1965           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
          15          148          115          197          271          392 
TCGA-99-8028 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
         459          154          114          282          238          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         116            6          285          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC 
        1951         1954         1954         1957         1980         1944 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                 2 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2146              2696 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              497               455 
[1] "1.0 - 2146.0 (497.0)" "2.0 - 2696.0 (455.0)"
[1] "hr=" "1.2"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  4Q LOSS MUTATED         2       32       33        10        10         21
  4Q LOSS WILD-TYPE       2       81       98        33        59         46
                   vv
clus                STAGE IIIB STAGE IV
  4Q LOSS MUTATED            5        8
  4Q LOSS WILD-TYPE          6       15
D48V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                32                81
  STAGE IB                33                98
  STAGE IIA               10                33
  STAGE IIB               10                59
  STAGE IIIA              21                46
  STAGE IIIB               5                 6
  STAGE IV                 8                15
[1] 8 2
[1] 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    38  67   9   5
  4Q LOSS WILD-TYPE 105 192  31  13
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              38               105
  T2              67               192
  T3               9                31
  T4               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                 N0  N1 N2+N3
  4Q LOSS MUTATED    79  13    25
  4Q LOSS WILD-TYPE 216  72    47
D48V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0                 79               216
  N1                 13                72
  N2+N3              25                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  4Q LOSS MUTATED    80   7   0   1  31
  4Q LOSS WILD-TYPE 237  11   1   2  88
D48V6, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               80               237
  M1                7                11
  M1A               0                 1
  M1B               1                 2
  MX               31                88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    61  60
  4Q LOSS WILD-TYPE 187 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     61   60
  4Q LOSS WILD-TYPE  187  154
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              61               187
  MALE                60               154
[1] 2 2
[1] FALSE
D48V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4Q LOSS MUTATED                            3
  4Q LOSS WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4Q LOSS MUTATED                                  21
  4Q LOSS WILD-TYPE                                72
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                   86
  4Q LOSS WILD-TYPE                                                208
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4Q LOSS MUTATED                                            0
  4Q LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  4Q LOSS MUTATED                                               3
  4Q LOSS WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  4Q LOSS MUTATED                                1
  4Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  4Q LOSS MUTATED                                    1
  4Q LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  4Q LOSS MUTATED                              0                             2
  4Q LOSS WILD-TYPE                            2                            17
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  4Q LOSS MUTATED                                 1
  4Q LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  4Q LOSS MUTATED                                               1
  4Q LOSS WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  4Q LOSS MUTATED                              2
  4Q LOSS WILD-TYPE                            5
D48V9, multiclass
                                                    clus
vv                                                   4Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              86
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   4Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 72
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               208
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     17
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  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     6 115
  4Q LOSS WILD-TYPE  15 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      6  115
  4Q LOSS WILD-TYPE   15  326
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                6                15
  YES             115               326
[1] 2 2
[1] FALSE
D48V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED    80   4   2   8
  4Q LOSS WILD-TYPE 238   7   2  11
D48V12, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              80               238
  R1               4                 7
  R2               2                 2
  RX               8                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                          10    91
  4Q LOSS WILD-TYPE                        16   271
D48V13, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                     10                16
  WHITE                                         91               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"
D48V14, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     2  91
  4Q LOSS WILD-TYPE   5 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   91
  4Q LOSS WILD-TYPE    5  241
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              91               241
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    31   2
  5P LOSS WILD-TYPE 290  80
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               33               370 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                80 
$`5P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4420 TCGA-05-4432 TCGA-35-4122 TCGA-35-4123 
        1523          607          912          761          225          182 
TCGA-44-6144 TCGA-44-6145 TCGA-44-8120 TCGA-49-6742 TCGA-55-1596 TCGA-55-7281 
         723          328          260          445         1375           18 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8505 TCGA-55-A492 TCGA-62-8398 TCGA-64-5779 
           3           31           29            1         1970          864 
TCGA-67-3771 TCGA-67-3772 TCGA-69-7979 TCGA-69-8255 TCGA-75-7027 TCGA-78-7160 
         610          573           89          129         1956          678 
TCGA-78-7161 TCGA-86-7713 TCGA-86-7955 TCGA-86-8074 TCGA-91-6829 TCGA-95-7043 
         215          422          508           24         1940            2 
TCGA-97-8175 TCGA-MN-A4N1 TCGA-MN-A4N4 
          87          285          622 

$`5P LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         426         1369         1126         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
         610         1958         1997          455          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 
         669          791          791          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         151          882          670           30           62           14 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
         264         1952         1962         1147         1492          864 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
        1073          354         1357          448         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
        1324         1429          400         1367          741         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6146 
         190          722         1013          863          383          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
        1864         1978          444          592          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         557         1970          882          535          719          385 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
          99          486          466          287          337          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         415           76         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
         999          268          896          157         1700          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         890          522          354         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         785          944         1499          246          282          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         686         1015          255          105         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 
         424          280          701         1178         1479           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
           2          993           24         1239           25         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 
          67         1826         1233         2151         1170           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
          39           39           34           24           54           19 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          16          197           21            5           33           21 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
         100            6           43           26            4           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
          15           33           46           66          216           44 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          23           11            8           15          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
           3          146          202          536           15           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
          49           66          106           33           42           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          48         1952           28            5           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
        1216         1289         2696         1445         2067         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        1246          910         1728          628         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 
        1126         1968         1959           62         1305         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         866           31          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         230          184           70          382          100           77 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         214           61         1600          711          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         467          131           40          164           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
         519         1970         1967         1965         1973         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1950         1944         1093         1963         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 
        1948         1957         1961         1963         1221         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1950         1934         1937         1965         1972         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1944          327          881         1952          994         1949 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1971         1981         1954         1964         1965         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
         824         1959           11          630         1968          591 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
        1963          745           10         1963           13          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
         489          476          482           16         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          26           35           45           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
         455          405           10           30           14           39 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
         323           60          310           79          417          372 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         842          224           35          492          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
          36           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
          34          568          377          477          476          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         964         1965         1932         1332          775          181 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 
          22          107          182         1965          147           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
         148          115          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         282          238          578          435          116            6 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
         353         1946         1967         1951         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1957         1980         1951         1944         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                 2 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1970              2696 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            422.0             471.5 
[1] "1.0 - 1970.0 (422.0)" "2.0 - 2696.0 (471.5)"
[1] "hr=" "1.6"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  5P LOSS MUTATED         0       10       11         4         8          3
  5P LOSS WILD-TYPE       4      103      120        39        61         64
                   vv
clus                STAGE IIIB STAGE IV
  5P LOSS MUTATED            0        2
  5P LOSS WILD-TYPE         11       21
D49V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                10               103
  STAGE IB                11               120
  STAGE IIA                4                39
  STAGE IIB                8                61
  STAGE IIIA               3                64
  STAGE IIIB               0                11
  STAGE IV                 2                21
[1] 8 2
[1] 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    13  20   3   1
  5P LOSS WILD-TYPE 130 239  37  17
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              13               130
  T2              20               239
  T3               3                37
  T4               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                 N0  N1 N2+N3
  5P LOSS MUTATED    26   8     4
  5P LOSS WILD-TYPE 269  77    68
D49V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                 26               269
  N1                  8                77
  N2+N3               4                68
[1] 3 2
[1] 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 M1B  MX
  5P LOSS MUTATED    28   2   0   0   8
  5P LOSS WILD-TYPE 289  16   1   3 111
D49V6, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               28               289
  M1                2                16
  M1A               0                 1
  M1B               0                 3
  MX                8               111
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    13  25
  5P LOSS WILD-TYPE 235 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     13   25
  5P LOSS WILD-TYPE  235  189
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              13               235
  MALE                25               189
[1] 2 2
[1] FALSE
D49V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5P LOSS MUTATED                            2
  5P LOSS WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5P LOSS MUTATED                                   8
  5P LOSS WILD-TYPE                                85
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                   24
  5P LOSS WILD-TYPE                                                270
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5P LOSS MUTATED                                            0
  5P LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  5P LOSS MUTATED                                               1
  5P LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  5P LOSS MUTATED                                0
  5P LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  5P LOSS MUTATED                                    0
  5P LOSS WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  5P LOSS MUTATED                              0                             0
  5P LOSS WILD-TYPE                            2                            19
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  5P LOSS MUTATED                                 0
  5P LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  5P LOSS MUTATED                                               2
  5P LOSS WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  5P LOSS MUTATED                              1
  5P LOSS WILD-TYPE                            6
D49V9, multiclass
                                                    clus
vv                                                   5P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              24
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   5P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               270
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     19
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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     1  37
  5P LOSS WILD-TYPE  20 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   37
  5P LOSS WILD-TYPE   20  404
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                1                20
  YES              37               404
[1] 2 2
[1] FALSE
D49V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    25   1   0   2
  5P LOSS WILD-TYPE 293  10   4  17
D49V12, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              25               293
  R1               1                10
  R2               0                 4
  RX               2                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     1
  5P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           3    28
  5P LOSS WILD-TYPE                        23   334
D49V13, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      3                23
  WHITE                                         28               334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     1  27
  5P LOSS WILD-TYPE   6 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   27
  5P LOSS WILD-TYPE    6  305
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              27               305
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   103  17
  5Q LOSS WILD-TYPE 218  65
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              120               283 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               17                65 
$`5Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4396 TCGA-05-4405 TCGA-05-4410 
        1523          607         1369         1947          610         1958 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-5425 
         455          912          913          791          761          882 
TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4628 
         670           62          225          182         1952         1492 
TCGA-38-4630 TCGA-38-4631 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
        1073          354         1013          863          723          328 
TCGA-44-6146 TCGA-44-6775 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
         302          705         1864          592          218          557 
TCGA-44-7670 TCGA-44-8120 TCGA-44-A4SS TCGA-49-4505 TCGA-49-6742 TCGA-50-5045 
         882          260          415          428          445         2174 
TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5941 TCGA-50-5946 TCGA-53-7624 
        2146          944         1499          567          686         1986 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6969 
         280          701         1178         1375           87         1239 
TCGA-55-6985 TCGA-55-7281 TCGA-55-7570 TCGA-55-7726 TCGA-55-7727 TCGA-55-7907 
        1233           18            6           39           34           16 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8094 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
           3           31            4           23           29           11 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
           8          228            9           15           48           66 
TCGA-55-A48Y TCGA-55-A491 TCGA-55-A492 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 
          42         1952            1         1216         1970         2696 
TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 
        1445         1246         1728         1686         1968         1305 
TCGA-64-5779 TCGA-67-3771 TCGA-67-3772 TCGA-69-7765 TCGA-69-7979 TCGA-69-8255 
         864          610          573          165           89          129 
TCGA-71-6725 TCGA-73-4668 TCGA-75-7027 TCGA-78-7149 TCGA-78-7150 TCGA-78-7159 
          61          467         1956         1093         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 TCGA-86-6851 TCGA-86-7713 TCGA-86-7953 
         678          215         1937         1959          422          591 
TCGA-86-7955 TCGA-86-8073 TCGA-86-8074 TCGA-86-8279 TCGA-86-8585 TCGA-86-8672 
         508           13           24          482           35           15 
TCGA-91-6829 TCGA-91-6840 TCGA-91-8499 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
        1940          372           36          186           34            2 
TCGA-95-7567 TCGA-95-7948 TCGA-97-7937 TCGA-97-8175 TCGA-99-8025 TCGA-J2-A4AD 
         568          476          181           87          427          287 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A5C7 
           6          285          622         1944         1970         1490 

$`5Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4422 
         426         1126         1431          578         1997          365 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
         669          791          761          730          457          151 
TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
          30           14          264         1962         1147          864 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1357          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5645 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 
         383          845          704          658         1938         1942 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 
        1978          444          366         1970          535          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
         385           99          486          466          287          337 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 
         351           76         1932         1081         1421          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
         268          896          157         1700          369          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 
         522          354          455          785          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 
         267         1091         2370          653          883          764 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1595 
        1015          255          105         1971          424         1479 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
           2          993           24           25         1475           67 
TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
        1826         2151         1170           35          121            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 
          95           40         1958           39           24           54 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          19          197           21            5           33           21 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
         100            6           43           26           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8508 
          33           46           66          216           44           15 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 
           3          146          202          536           49          106 
TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          33           29           48           28            5           47 
TCGA-55-A4DG TCGA-62-8397 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 
         162         1289         2067         2199          910          628 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 
        1189         1126         1959           62         1559          866 
TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
          31          427          385          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 
         202          186          690          414          230          184 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 
          70          382          100           77          214         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         711          912          800          131           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 
          38          621          519         1970         1967         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 
        1973         1988         1950         1944         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 
        1948         1957         1961         1963         1940         1950 
TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1934         1965         1972         1949         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881         1952          994         1949         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 
        1954         1964         1965         1972          824           11 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
         630         1968         1963          745           10         1963 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
         479          489          476           16         1955           19 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
          26           45           34           18          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
          10           30           14           39          323           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
         310           79          417          842          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         492          197          174           44          218          297 
TCGA-93-7348 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
         127          377          477          121          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932         1332          775           22          107          182 
TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
        1965          147           15          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         271          392          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         114          282          238          578          435          116 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
         353         1946         1967         1951         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1957         1980         1951         1970          142         1955 
TCGA-MP-A4TK 
        1971 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                 2 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2696              2370 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            567.5             444.0 
[1] "1.0 - 2696.0 (567.5)" "2.0 - 2370.0 (444.0)"
[1] "hr=" "1.4"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  5Q LOSS MUTATED         0       30       40        13        25         15
  5Q LOSS WILD-TYPE       4       83       91        30        44         52
                   vv
clus                STAGE IIIB STAGE IV
  5Q LOSS MUTATED            3        7
  5Q LOSS WILD-TYPE          8       16
D50V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                30                83
  STAGE IB                40                91
  STAGE IIA               13                30
  STAGE IIB               25                44
  STAGE IIIA              15                52
  STAGE IIIB               3                 8
  STAGE IV                 7                16
[1] 8 2
[1] 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    39  76  12   5
  5Q LOSS WILD-TYPE 104 183  28  13
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              39               104
  T2              76               183
  T3              12                28
  T4               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                 N0  N1 N2+N3
  5Q LOSS MUTATED    86  29    17
  5Q LOSS WILD-TYPE 209  56    55
D50V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                 86               209
  N1                 29                56
  N2+N3              17                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  5Q LOSS MUTATED    89   4   0   2  37
  5Q LOSS WILD-TYPE 228  14   1   1  82
D50V6, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               89               228
  M1                4                14
  M1A               0                 1
  M1B               2                 1
  MX               37                82
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    59  74
  5Q LOSS WILD-TYPE 189 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     59   74
  5Q LOSS WILD-TYPE  189  140
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              59               189
  MALE                74               140
[1] 2 2
[1] FALSE
D50V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5Q LOSS MUTATED                            4
  5Q LOSS WILD-TYPE                          9
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5Q LOSS MUTATED                                  31
  5Q LOSS WILD-TYPE                                62
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                   84
  5Q LOSS WILD-TYPE                                                210
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5Q LOSS MUTATED                                            0
  5Q LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  5Q LOSS MUTATED                                               3
  5Q LOSS WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  5Q LOSS MUTATED                                0
  5Q LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  5Q LOSS MUTATED                                    2
  5Q LOSS WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  5Q LOSS MUTATED                              1                             4
  5Q LOSS WILD-TYPE                            1                            15
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  5Q LOSS MUTATED                                 0
  5Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  5Q LOSS MUTATED                                               3
  5Q LOSS WILD-TYPE                                             1
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  5Q LOSS MUTATED                              1
  5Q LOSS WILD-TYPE                            6
D50V9, multiclass
                                                    clus
vv                                                   5Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              84
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   5Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               210
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     15
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      1
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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     4 129
  5Q LOSS WILD-TYPE  17 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4  129
  5Q LOSS WILD-TYPE   17  312
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                4                17
  YES             129               312
[1] 2 2
[1] FALSE
D50V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    88   3   0  10
  5Q LOSS WILD-TYPE 230   8   4   9
D50V12, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              88               230
  R1               3                 8
  R2               0                 4
  RX              10                 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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1     3
  5Q LOSS WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          10   101
  5Q LOSS WILD-TYPE                        16   261
D50V13, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 3
  BLACK OR AFRICAN AMERICAN                     10                16
  WHITE                                        101               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"
D50V14, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5  95
  5Q LOSS WILD-TYPE   2 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5   95
  5Q LOSS WILD-TYPE    2  237
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO              95               237
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    59  25
  6P LOSS WILD-TYPE 262  57
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               84               319 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               25                57 
$`6P LOSS MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-35-4123 TCGA-38-4631 TCGA-38-4632 
        1369         1126         1997          182          354         1357 
TCGA-38-6178 TCGA-44-2662 TCGA-44-2668 TCGA-44-6775 TCGA-44-6777 TCGA-44-A47F 
         448         1280          246          705         1942          337 
TCGA-49-4486 TCGA-49-4505 TCGA-49-4512 TCGA-49-6745 TCGA-50-5051 TCGA-50-5068 
        1932          428          157          522          455         1499 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-53-7626 TCGA-55-6971 TCGA-55-6972 
        1091          653         1015         1971           25         1475 
TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 TCGA-55-7576 TCGA-55-7724 TCGA-55-7815 
        1826         1233           35           40         1958           54 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 
         100            6           43           66           23           11 
TCGA-55-8508 TCGA-55-8616 TCGA-55-A48X TCGA-55-A494 TCGA-62-8402 TCGA-62-A472 
          15           48           33            5         1445          910 
TCGA-64-1676 TCGA-64-5781 TCGA-69-7760 TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 
        1728         1559          202          184          100           77 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-75-7025 TCGA-78-7146 
         214          711          800           40         1967         1988 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7158 TCGA-78-7535 TCGA-78-7536 
        1202          760         1948         1963         1972         1949 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
         824           11          422          591          508          745 
TCGA-86-8359 TCGA-86-8672 TCGA-91-6831 TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 
          26           15          310          297          127            2 
TCGA-95-7948 TCGA-97-7547 TCGA-97-8174 TCGA-97-8547 TCGA-99-7458 TCGA-J2-8192 
         476         1965         1965          148          392          154 
TCGA-MN-A4N1 TCGA-MP-A4T2 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TK TCGA-MP-A5C7 
         285         1951         1944         1970         1971         1490 

$`6P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        1523          607          426         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
         610         1958          455          912          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         669          791          791          761          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         457          151          882          670           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
          14          225          264         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
        1492          864         1073         1971          133         1324 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 
        1429          400         1367          741         1301           97 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1130         1163         1036          190          722         1013 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         863          383          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         704          658         1938         1864         1978          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         592          366          218          557         1970          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         535          719          385           99          260          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 
         466          287          351          415           76         1081 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 
        1421          999          268          896         1700          445 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
         369          890          354         2174         2146          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 
         944          246          282          267         2370          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         883          764          686          255          105         1986 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
         424          280          701         1178         1479         1375 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 
          87            2          993           24         1239           67 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        2151         1170           18          121            6            4 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 
          95           39           39           34           24           19 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          16          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
          33           21           26            4           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 
          33           46          216           44           29            8 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
          15           49           66          106           42           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
          48         1952            1           28           47          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V 
        1216         1289         1970         2696         2067         2199 
TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        1246          628         1189         1686         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 
        1959           62         1305          864          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         610          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
         422          186          690          414          165          230 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 
          70           89          382          129           61         1600 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         912          467          131          164           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 
         519         1970         1956         1965         1973         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 
        1944         1093         1963         1957         1961         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          215         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1965         1944          327          881         1952          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
        1949         1971         1981         1954         1964         1965 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8055 
        1972         1959          630         1968         1963           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        1963           13           24          479          489          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
         482           16         1955           19           35           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          34           18          455          405           10           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
          14           39          323         1940           60           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
         417          372          842          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-8067 
         197          174           36           44          218          186 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 
          34          568          377          477          121          964 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
        1932         1332          775          181           22          107 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 
         182           87          147           15          115          197 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
         271          427          459           44          170          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         287          282          238          578          435          116 
TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
           6          622          353         1946         1967         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH 
        1954         1957         1980         1951         1970          142 
TCGA-MP-A4TI 
        1955 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                 1 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             1997              2696 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              515               457 
[1] "2.0 - 1997.0 (515.0)" "1.0 - 2696.0 (457.0)"
[1] "hr=" "1.6"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  6P LOSS MUTATED         0       14       32         8        14         19
  6P LOSS WILD-TYPE       4       99       99        35        55         48
                   vv
clus                STAGE IIIB STAGE IV
  6P LOSS MUTATED            3        4
  6P LOSS WILD-TYPE          8       19
D51V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                14                99
  STAGE IB                32                99
  STAGE IIA                8                35
  STAGE IIB               14                55
  STAGE IIIA              19                48
  STAGE IIIB               3                 8
  STAGE IV                 4                19
[1] 8 2
[1] 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  60  10   4
  6P LOSS WILD-TYPE 123 199  30  14
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              20               123
  T2              60               199
  T3              10                30
  T4               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                 N0  N1 N2+N3
  6P LOSS MUTATED    57  17    19
  6P LOSS WILD-TYPE 238  68    53
D51V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0                 57               238
  N1                 17                68
  N2+N3              19                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  6P LOSS MUTATED    63   4   0   0  26
  6P LOSS WILD-TYPE 254  14   1   3  93
D51V6, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               63               254
  M1                4                14
  M1A               0                 1
  M1B               0                 3
  MX               26                93
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    48  47
  6P LOSS WILD-TYPE 200 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     48   47
  6P LOSS WILD-TYPE  200  167
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              48               200
  MALE                47               167
[1] 2 2
[1] FALSE
D51V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6P LOSS MUTATED                            3
  6P LOSS WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6P LOSS MUTATED                                  18
  6P LOSS WILD-TYPE                                75
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                   64
  6P LOSS WILD-TYPE                                                230
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6P LOSS MUTATED                                            0
  6P LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  6P LOSS MUTATED                                               2
  6P LOSS WILD-TYPE                                            17
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  6P LOSS MUTATED                                0
  6P LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  6P LOSS MUTATED                                    1
  6P LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  6P LOSS MUTATED                              0                             4
  6P LOSS WILD-TYPE                            2                            15
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  6P LOSS MUTATED                                 0
  6P LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  6P LOSS MUTATED                                               1
  6P LOSS WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  6P LOSS MUTATED                              2
  6P LOSS WILD-TYPE                            5
D51V9, multiclass
                                                    clus
vv                                                   6P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              64
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    2
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    4
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   6P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 75
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               230
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     17
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     15
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  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     5  90
  6P LOSS WILD-TYPE  16 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   90
  6P LOSS WILD-TYPE   16  351
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                5                16
  YES              90               351
[1] 2 2
[1] FALSE
D51V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    68   3   1   4
  6P LOSS WILD-TYPE 250   8   3  15
D51V12, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              68               250
  R1               3                 8
  R2               1                 3
  RX               4                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     0
  6P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           6    77
  6P LOSS WILD-TYPE                        20   285
D51V13, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 6
  BLACK OR AFRICAN AMERICAN                      6                20
  WHITE                                         77               285
[1] 4 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     1  70
  6P LOSS WILD-TYPE   6 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   70
  6P LOSS WILD-TYPE    6  262
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              70               262
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   130  44
  6Q LOSS WILD-TYPE 191  38
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              174               229 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               44                38 
$`6Q LOSS MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4405 TCGA-05-4415 TCGA-05-4425 
         607         1369         1126          610         1997          669 
TCGA-05-4430 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-38-4631 
         761          670           30           14          182          354 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-2666 
        1357          448         1429         1367         1280           97 
TCGA-44-2668 TCGA-44-3918 TCGA-44-5644 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 
         246         1036          863          845          658          705 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F 
        1942         1978          444          385          260          337 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 
          76         1932         1081          428          268          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5051 
         157         1700          890          522          354          455 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
        1499         1091         2370          653          567          883 
TCGA-50-5946 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1595 TCGA-55-6543 
         686         1986         1971          424         1479            2 
TCGA-55-6642 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 
         993           25         1475         1826         1233           35 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
          40         1958           39           54           19           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           3           31           33          100            6           43 
TCGA-55-8094 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 
           4           66           23           11           15            3 
TCGA-55-8615 TCGA-55-8616 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A494 TCGA-62-8395 
          15           48           33           42            5         1216 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
        1970         1445         2199          910         1728          628 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        1189         1959          864         1559          866          610 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 
         141          202          230          184           70          100 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-7498 
         214         1600          711          800           40          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7149 
         519         1970         1967         1956         1988         1093 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1202          760         1948         1961         1963         1221 
TCGA-78-7162 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
        1940         1972         1949         1944          881         1952 
TCGA-78-7633 TCGA-78-8655 TCGA-80-5607 TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 
         994         1981         1965          824           11          422 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8279 TCGA-86-8280 
        1968          591          508          745          482           16 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
        1955           19           26           15          405           10 
TCGA-91-6831 TCGA-91-7771 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 
         310          492          218          297          127            2 
TCGA-95-7567 TCGA-95-7948 TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 
         568          476         1965          775          181         1965 
TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-J2-8192 TCGA-J2-8194 
         148          197          271          392          154          114 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
         578          116            6          285          353         1946 
TCGA-MP-A4T2 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1944         1970         1970         1971         1490 

$`6Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4410 
        1523          426         1947         1431          578         1958 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 
         455          912          365          913          791          791 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5715 
         761          730          457          151          882           62 
TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         225          264         1952         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 
         864         1073         1971          133         1324          400 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
         741         1301         1130         1163          190          722 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
        1013          383          723          328          302          704 
TCGA-44-6776 TCGA-44-6778 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
        1938         1864          592          366          218          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
        1970          882          535          719           99          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4501 TCGA-49-4506 
         466          287          351          415         1421          999 
TCGA-49-6742 TCGA-49-6743 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         445          369         2174         2146          785          944 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 
         246          282          267          764         1015          255 
TCGA-50-8460 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
         105          280          701         1178         1375           87 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
          24         1239           67         2151         1170           18 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7726 TCGA-55-7727 
         121            6            4           95           39           34 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8087 TCGA-55-8092 
          24           16          197            5           21           26 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 
          47           15           33           46          216           44 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 
          29            8          228            9          146          202 
TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Z TCGA-55-A490 
         536           49           66          106           29           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 
        1952            1           28           47          162         1289 
TCGA-62-8399 TCGA-62-A46U TCGA-62-A471 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        2696         2067         1246         1686         1126         1968 
TCGA-64-5775 TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
          62         1305           31          573          427          385 
TCGA-67-6215 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         174          422          186          690          414          165 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4662 
          89          382           77          129           61          912 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-75-7031 TCGA-78-7145 
         467          131          164           38         1965         1973 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 
        1950         1944         1963         1957          678          215 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-8640 
        1950         1934         1937         1965          327         1949 
TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 
        1971         1954         1964         1972         1959          630 
TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
        1963           10         1963           13           24          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
         489          476           35           45           34           18 
TCGA-86-8673 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
         455           30           14           39          323         1940 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
          60           79          417          372          842          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 
          35          197          174           36           44          186 
TCGA-95-7039 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 
          34          377          477          121          964         1932 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 
        1332           22          107          182           87          147 
TCGA-97-8179 TCGA-97-8552 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
          15          115          427          459           44          170 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MP-A4SW 
         287          282          238          435          622         1967 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH 
        1954         1954         1957         1980         1951          142 
TCGA-MP-A4TI 
        1955 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                 1 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             2370              2696 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              610               415 
[1] "2.0 - 2370.0 (610.0)" "1.0 - 2696.0 (415.0)"
[1] "hr=" "1.2"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  6Q LOSS MUTATED         1       42       57        19        25         34
  6Q LOSS WILD-TYPE       3       71       74        24        44         33
                   vv
clus                STAGE IIIB STAGE IV
  6Q LOSS MUTATED            6       10
  6Q LOSS WILD-TYPE          5       13
D52V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                42                71
  STAGE IB                57                74
  STAGE IIA               19                24
  STAGE IIB               25                44
  STAGE IIIA              34                33
  STAGE IIIB               6                 5
  STAGE IV                10                13
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q LOSS MUTATED    57 108  20   8
  6Q LOSS WILD-TYPE  86 151  20  10
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              57                86
  T2             108               151
  T3              20                20
  T4               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                 N0  N1 N2+N3
  6Q LOSS MUTATED   121  34    35
  6Q LOSS WILD-TYPE 174  51    37
D52V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                121               174
  N1                 34                51
  N2+N3              35                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  6Q LOSS MUTATED   132   8   0   2  50
  6Q LOSS WILD-TYPE 185  10   1   1  69
D52V6, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              132               185
  M1                8                10
  M1A               0                 1
  M1B               2                 1
  MX               50                69
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    99  95
  6Q LOSS WILD-TYPE 149 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     99   95
  6Q LOSS WILD-TYPE  149  119
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              99               149
  MALE                95               119
[1] 2 2
[1] FALSE
D52V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6Q LOSS MUTATED                            5
  6Q LOSS WILD-TYPE                          8
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6Q LOSS MUTATED                                  43
  6Q LOSS WILD-TYPE                                50
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                  122
  6Q LOSS WILD-TYPE                                                172
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6Q LOSS MUTATED                                            2
  6Q LOSS WILD-TYPE                                          2
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  6Q LOSS MUTATED                                               7
  6Q LOSS WILD-TYPE                                            12
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  6Q LOSS MUTATED                                1
  6Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  6Q LOSS MUTATED                                    2
  6Q LOSS WILD-TYPE                                  2
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  6Q LOSS MUTATED                              0                             9
  6Q LOSS WILD-TYPE                            2                            10
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  6Q LOSS MUTATED                                 0
  6Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  6Q LOSS MUTATED                                               1
  6Q LOSS WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  6Q LOSS MUTATED                              2
  6Q LOSS WILD-TYPE                            5
D52V9, multiclass
                                                    clus
vv                                                   6Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             122
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    7
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               2
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    9
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   6Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               172
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     12
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 2
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     10
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  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    10 184
  6Q LOSS WILD-TYPE  11 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     10  184
  6Q LOSS WILD-TYPE   11  257
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               10                11
  YES             184               257
[1] 2 2
[1] FALSE
D52V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED   141   4   1   7
  6Q LOSS WILD-TYPE 177   7   3  12
D52V12, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0             141               177
  R1               4                 7
  R2               1                 3
  RX               7                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     2
  6Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                          11   155
  6Q LOSS WILD-TYPE                        15   207
D52V13, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                     11                15
  WHITE                                        155               207
[1] 4 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     3 139
  6Q LOSS WILD-TYPE   4 193
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  139
  6Q LOSS WILD-TYPE    4  193
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             139               193
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    23   6
  7P LOSS WILD-TYPE 298  76
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               29               374 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6                76 
$`7P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4427 TCGA-38-4630 TCGA-44-5643 TCGA-44-6145 TCGA-44-7670 
        1523          791         1073         1013          328          882 
TCGA-44-8119 TCGA-44-A47B TCGA-49-6742 TCGA-50-5931 TCGA-53-7813 TCGA-55-1594 
          99          287          445          267          424         1178 
TCGA-55-8507 TCGA-62-A471 TCGA-67-3770 TCGA-67-3774 TCGA-69-7763 TCGA-73-4659 
           8         1246           31          385          690          711 
TCGA-78-7167 TCGA-78-7220 TCGA-86-8278 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6840 
        1937         1965          476           30          323          372 
TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 TCGA-95-7039 TCGA-97-8174 
         492           36          186           34         1965 

$`7P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
         607          426         1369         1126         1947         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
         365          913          669          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
         730          457          151          882          670           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 
        1962         1147         1492          864          354         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
         448         1971          133         1324         1429          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1367          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
        1130         1163         1036          190          722          863 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         383          723          302          845          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         705         1938         1942         1864         1978          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
         592          366          218          557         1970          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F 
         719          385          260          486          466          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         351          415           76         1932         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
         428          999          268          896          157         1700 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
         369          890          522          354         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         686         1015          255          105         1986         1971 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
         280          701         1479         1375           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
         993           24         1239           25         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1826         1233         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40         1958 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
          39           39           34           24           54           19 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          16          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33           21          100            6           43           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           4           47           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
         216           44           23           29           11           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
          15           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          42           29           48         1952            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           5           47          162         1216         1289         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 
        2696         1445         2067         2199          910         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
         628         1189         1686         1126         1968         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
          62         1305          864         1559          866          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         573          427          174          141          422          202 
TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         186          414          165          230          184           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          89          382          100           77          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
          61         1600          912          800          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 
          40          164           38          621          519         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1967         1956         1965         1973         1988         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1944         1093         1963         1202          760         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1957         1961         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        1940         1950         1934         1972         1949         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
         327          881         1952          994         1949         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
        1981         1954         1964         1965         1972          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        1959           11          630          422         1968          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
        1963          508          745           10         1963           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
          24          479          489          482           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          19           26           35           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
          15          455          405           10           14           39 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 
        1940           60          310           79          417          842 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
         224           35          197          174           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
         297          127            2          568          377          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         476          121          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
         775          181           22          107          182           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
         147           15          148          115          197          271 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         392          427          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         116            6          285          622          353         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1967         1951         1954         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1951         1944         1970         1970          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8                 1 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1965              2696 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            445.0             466.5 
[1] "8.0 - 1965.0 (445.0)" "1.0 - 2696.0 (466.5)"
[1] "hr=" "1.9"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  7P LOSS MUTATED         0        7        7         3         7          4
  7P LOSS WILD-TYPE       4      106      124        40        62         63
                   vv
clus                STAGE IIIB STAGE IV
  7P LOSS MUTATED            1        1
  7P LOSS WILD-TYPE         10       22
D53V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                 7               106
  STAGE IB                 7               124
  STAGE IIA                3                40
  STAGE IIB                7                62
  STAGE IIIA               4                63
  STAGE IIIB               1                10
  STAGE IV                 1                22
[1] 8 2
[1] 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     8  18   3   1
  7P LOSS WILD-TYPE 135 241  37  17
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               8               135
  T2              18               241
  T3               3                37
  T4               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                 N0  N1 N2+N3
  7P LOSS MUTATED    21   5     4
  7P LOSS WILD-TYPE 274  80    68
D53V5, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0                 21               274
  N1                  5                80
  N2+N3               4                68
[1] 3 2
[1] 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 M1B  MX
  7P LOSS MUTATED    24   1   0   0   5
  7P LOSS WILD-TYPE 293  17   1   3 114
D53V6, multiclass
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               24               293
  M1                1                17
  M1A               0                 1
  M1B               0                 3
  MX                5               114
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    13  17
  7P LOSS WILD-TYPE 235 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     13   17
  7P LOSS WILD-TYPE  235  197
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE              13               235
  MALE                17               197
[1] 2 2
[1] FALSE
D53V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7P LOSS MUTATED                            0
  7P LOSS WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7P LOSS MUTATED                                   4
  7P LOSS WILD-TYPE                                89
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                   21
  7P LOSS WILD-TYPE                                                273
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7P LOSS MUTATED                                            0
  7P LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  7P LOSS MUTATED                                               1
  7P LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  7P LOSS MUTATED                                0
  7P LOSS WILD-TYPE                              2
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  7P LOSS MUTATED                                    0
  7P LOSS WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  7P LOSS MUTATED                              0                             3
  7P LOSS WILD-TYPE                            2                            16
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  7P LOSS MUTATED                                 0
  7P LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  7P LOSS MUTATED                                               0
  7P LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  7P LOSS MUTATED                              1
  7P LOSS WILD-TYPE                            6
D53V9, multiclass
                                                    clus
vv                                                   7P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              21
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   7P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               273
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     16
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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  28
  7P LOSS WILD-TYPE  19 413
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2   28
  7P LOSS WILD-TYPE   19  413
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                2                19
  YES              28               413
[1] 2 2
[1] FALSE
D53V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    17   1   0   2
  7P LOSS WILD-TYPE 301  10   4  17
D53V12, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              17               301
  R1               1                10
  R2               0                 4
  RX               2                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     1
  7P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           1    25
  7P LOSS WILD-TYPE                        25   337
D53V13, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      1                25
  WHITE                                         25               337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  24
  7P LOSS WILD-TYPE   6 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   24
  7P LOSS WILD-TYPE    6  308
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              24               308
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    28   4
  7Q LOSS WILD-TYPE 293  78
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               32               371 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                78 
$`7Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4417 TCGA-05-4427 TCGA-38-4630 TCGA-44-5643 
        1523         1369          455          791         1073         1013 
TCGA-44-7670 TCGA-44-8119 TCGA-44-A47B TCGA-49-6742 TCGA-50-5931 TCGA-53-7813 
         882           99          287          445          267          424 
TCGA-55-1594 TCGA-55-1595 TCGA-55-7727 TCGA-55-A491 TCGA-55-A4DG TCGA-62-8402 
        1178         1479           34         1952          162         1445 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3774 TCGA-75-6214 TCGA-75-7025 TCGA-86-8278 
          31          610          385         1970         1967          476 
TCGA-91-6828 TCGA-91-6840 TCGA-91-7771 TCGA-93-8067 TCGA-95-7039 TCGA-97-8174 
         323          372          492          186           34         1965 
TCGA-97-A4M7 TCGA-99-8032 
         271           44 

$`7Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
         607          426         1126         1947         1431          578 
TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
         610         1958         1997          912          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         669          791          761          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         151          882          670           30           62           14 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
         225          182          264         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
        1492          864          354         1357          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        1036          190          722          863          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         328          302          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
        1938         1942         1864         1978          444          592 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 
         366          218          557         1970          535          719 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G 
         385          260          486          466          337          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
         415           76         1932         1081         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
         999          268          896          157         1700          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         890          522          354         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
         785          944         1499          246          282         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        2370          653          567          883          764          686 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
        1015          255          105         1986         1971          280 
TCGA-55-1592 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
         701         1375           87            2          993           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
        1239           25         1475           67         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        2151         1170           18           35          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40         1958           39           39 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          24           54           19           16          197           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
           3           31            5           33           21          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
           6           43           26            4           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          29           11            8           15          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
           3          146          202          536           15           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
          49           66          106           33           42           29 
TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 
          48            1           28            5           47         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1289         1970         2696         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
         910         1728          628         1189         1686         1126 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1968         1959           62         1305          864         1559 
TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         866          573          427          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
         202          186          690          414          165          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         184           70           89          382          100           77 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
         129          214           61         1600          711          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
         800          467          131           40          164           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
         621          519         1956         1965         1973         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1950         1944         1093         1963         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
        1948         1957         1961         1963         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
         215         1940         1950         1934         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1972         1949         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         994         1949         1971         1981         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1965         1972          824         1959           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         422         1968          591         1963          508          745 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
          10         1963           13           24          479          489 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
         482           16         1955           19           26           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          45           34           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
          10           30           14           39         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
         310           79          417          842          224           35 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-93-7348 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
         127            2          568          377          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         121          964         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 
         181           22          107          182           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 
          15          148          115          197          392          427 
TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
         459          170          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         238          578          435          116            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         622          353         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               31                 1 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1970              2696 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            465.5             466.0 
[1] "31.0 - 1970.0 (465.5)" "1.0 - 2696.0 (466.0)" 
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  7Q LOSS MUTATED         0       11        9         2         7          5
  7Q LOSS WILD-TYPE       4      102      122        41        62         62
                   vv
clus                STAGE IIIB STAGE IV
  7Q LOSS MUTATED            1        0
  7Q LOSS WILD-TYPE         10       23
D54V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                 4
  STAGE IA                11               102
  STAGE IB                 9               122
  STAGE IIA                2                41
  STAGE IIB                7                62
  STAGE IIIA               5                62
  STAGE IIIB               1                10
  STAGE IV                 0                23
[1] 8 2
[1] 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    13  18   3   1
  7Q LOSS WILD-TYPE 130 241  37  17
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              13               130
  T2              18               241
  T3               3                37
  T4               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                 N0  N1 N2+N3
  7Q LOSS MUTATED    25   5     5
  7Q LOSS WILD-TYPE 270  80    67
D54V5, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0                 25               270
  N1                  5                80
  N2+N3               5                67
[1] 3 2
[1] 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 M1B  MX
  7Q LOSS MUTATED    29   0   0   0   6
  7Q LOSS WILD-TYPE 288  18   1   3 113
D54V6, multiclass
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               29               288
  M1                0                18
  M1A               0                 1
  M1B               0                 3
  MX                6               113
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    18  17
  7Q LOSS WILD-TYPE 230 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     18   17
  7Q LOSS WILD-TYPE  230  197
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              18               230
  MALE                17               197
[1] 2 2
[1] FALSE
D54V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7Q LOSS MUTATED                            0
  7Q LOSS WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7Q LOSS MUTATED                                   6
  7Q LOSS WILD-TYPE                                87
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                   24
  7Q LOSS WILD-TYPE                                                270
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7Q LOSS MUTATED                                            0
  7Q LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  7Q LOSS MUTATED                                               1
  7Q LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  7Q LOSS MUTATED                                1
  7Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  7Q LOSS MUTATED                                    0
  7Q LOSS WILD-TYPE                                  4
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  7Q LOSS MUTATED                              0                             2
  7Q LOSS WILD-TYPE                            2                            17
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  7Q LOSS MUTATED                                 0
  7Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  7Q LOSS MUTATED                                               0
  7Q LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  7Q LOSS MUTATED                              1
  7Q LOSS WILD-TYPE                            6
D54V9, multiclass
                                                    clus
vv                                                   7Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              24
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               0
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   7Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               270
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 4
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     17
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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  34
  7Q LOSS WILD-TYPE  20 407
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   34
  7Q LOSS WILD-TYPE   20  407
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1                20
  YES              34               407
[1] 2 2
[1] FALSE
D54V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    23   1   0   2
  7Q LOSS WILD-TYPE 295  10   4  17
D54V12, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              23               295
  R1               1                10
  R2               0                 4
  RX               2                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     2
  7Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           2    24
  7Q LOSS WILD-TYPE                        24   338
D54V13, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      2                24
  WHITE                                         24               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"
D54V14, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  25
  7Q LOSS WILD-TYPE   6 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   25
  7Q LOSS WILD-TYPE    6  307
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              25               307
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   123  30
  8P LOSS WILD-TYPE 198  52
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              153               250 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               30                52 
$`8P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4410 TCGA-05-4420 
        1523         1369         1126         1431         1958          912 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4427 TCGA-05-4433 TCGA-05-5425 TCGA-35-4122 
         365          669          791          730          882          225 
TCGA-35-4123 TCGA-38-4628 TCGA-38-4631 TCGA-44-2657 TCGA-44-2662 TCGA-44-2668 
         182         1492          354          400         1280          246 
TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
        1036          190         1013          863          723          328 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7660 TCGA-44-7662 TCGA-44-7670 
         658          705         1942          592          218          882 
TCGA-44-8117 TCGA-44-A479 TCGA-44-A4SU TCGA-49-4501 TCGA-49-4505 TCGA-49-4510 
         385          486           76         1421          428          896 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 
         369          890          354         2146          944         1499 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5941 TCGA-50-6597 TCGA-53-7624 TCGA-53-7626 
         267         1091          567         1015         1986         1971 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6980 TCGA-55-6985 
         280         1178         1479           87           67         1233 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7726 TCGA-55-7727 
          35            6            4           40           39           34 
TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8092 TCGA-55-8097 
          19            3           31            5           26           15 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8616 
          33           66           23           11          228           48 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U 
        1952           28          162         1216         1445         2067 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
        1728         1189         1686         1968           62         1305 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 
         866           31          610          573          422          202 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-73-4662 TCGA-73-4668 
          70           89          382          129          912          467 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7150 TCGA-78-7152 
         621          519         1970         1967         1963         1202 
TCGA-78-7155 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 
        1957         1949         1952         1949         1954         1964 
TCGA-86-6851 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
        1959          422          591         1963          745           10 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8359 TCGA-86-8668 TCGA-86-A456 
          24          479          482           26           45           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6836 TCGA-91-6847 TCGA-91-8499 TCGA-91-A4BD 
          30           14          417          842           36          218 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK 
         186           34            2          377          477          121 
TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8547 TCGA-97-A4M7 
         964          775          181          107          148          271 
TCGA-99-7458 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 
         392           44          154          114          282          578 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 
         622          353         1946         1967         1954         1954 
TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TK 
        1980         1944         1971 

$`8P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
         607          426         1947          578          610         1997 
TCGA-05-4417 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 
         455          913          791          761          761          457 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 
         151          670           30           62           14          264 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
        1952         1962         1147          864         1073         1357 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 
         448         1971          133         1324         1429         1367 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 
         741         1301           97         1130         1163          722 
TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6776 TCGA-44-6778 
         383          302          845          704         1938         1864 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
        1978          444          366          557         1970          535 
TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
         719           99          260          466          287          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 
         351          415         1932         1081          999          268 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-50-5045 TCGA-50-5051 
         157         1700          445          522         2174          455 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 
         785          246          282         2370          653          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-55-1592 
         764          686          255          105          424          701 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 
        1375            2          993           24         1239           25 
TCGA-55-6972 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 
        1475         1826         2151         1170           18          121 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
          95         1958           39           24           54           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
         197           21           33           21          100            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 
          43            4           47           46          216           44 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          29            8           15            9            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         202          536           15           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 
          33           42           29           48            1            5 
TCGA-55-A4DF TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 
          47         1289         1970         2696         2199         1246 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 
         910          628         1126         1959          864         1559 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
         427          385          174          141          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 
         414          165          230          184          100           77 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 
         214           61         1600          711          800          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
          40          164           38         1956         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 
        1988         1950         1944         1093          760         1948 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1961         1963         1221          678          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 
        1950         1934         1937         1965         1972         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-80-5607 
         327          881          994         1971         1981         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 
        1972          824           11          630         1968          508 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 
        1963           13          489          476           16         1955 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          19           35           34           18           15          455 
TCGA-86-8674 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
         405           39          323         1940           60          310 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
          79          372          224           35          492          197 
TCGA-91-8497 TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 TCGA-95-7567 TCGA-95-7948 
         174           44          297          127          568          476 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 
        1965         1932         1332           22          182         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8025 
          87          147           15          115          197          427 
TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
         459          170          287          238          435          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE 
           6          285         1951         1957         1951         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1970          142         1955         1490 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                 1 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             2146              2696 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              486               455 
[1] "2.0 - 2146.0 (486.0)" "1.0 - 2696.0 (455.0)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  8P LOSS MUTATED         2       45       50        17        29         25
  8P LOSS WILD-TYPE       2       68       81        26        40         42
                   vv
clus                STAGE IIIB STAGE IV
  8P LOSS MUTATED            3        7
  8P LOSS WILD-TYPE          8       16
D55V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  2                 2
  STAGE IA                45                68
  STAGE IB                50                81
  STAGE IIA               17                26
  STAGE IIB               29                40
  STAGE IIIA              25                42
  STAGE IIIB               3                 8
  STAGE IV                 7                16
[1] 8 2
[1] 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    60  99  13   5
  8P LOSS WILD-TYPE  83 160  27  13
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              60                83
  T2              99               160
  T3              13                27
  T4               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                 N0  N1 N2+N3
  8P LOSS MUTATED   113  34    28
  8P LOSS WILD-TYPE 182  51    44
D55V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                113               182
  N1                 34                51
  N2+N3              28                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  8P LOSS MUTATED   122   6   1   0  48
  8P LOSS WILD-TYPE 195  12   0   3  71
D55V6, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              122               195
  M1                6                12
  M1A               1                 0
  M1B               0                 3
  MX               48                71
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   106  72
  8P LOSS WILD-TYPE 142 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    106   72
  8P LOSS WILD-TYPE  142  142
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE             106               142
  MALE                72               142
[1] 2 2
[1] FALSE
D55V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8P LOSS MUTATED                            6
  8P LOSS WILD-TYPE                          7
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8P LOSS MUTATED                                  31
  8P LOSS WILD-TYPE                                62
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                  121
  8P LOSS WILD-TYPE                                                173
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8P LOSS MUTATED                                            1
  8P LOSS WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  8P LOSS MUTATED                                               7
  8P LOSS WILD-TYPE                                            12
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  8P LOSS MUTATED                                2
  8P LOSS WILD-TYPE                              0
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  8P LOSS MUTATED                                    4
  8P LOSS WILD-TYPE                                  0
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  8P LOSS MUTATED                              0                             3
  8P LOSS WILD-TYPE                            2                            16
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  8P LOSS MUTATED                                 1
  8P LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  8P LOSS MUTATED                                               2
  8P LOSS WILD-TYPE                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  8P LOSS MUTATED                              0
  8P LOSS WILD-TYPE                            7
D55V9, multiclass
                                                    clus
vv                                                   8P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             121
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    7
  LUNG CLEAR CELL ADENOCARCINOMA                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                               4
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    3
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    2
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   8P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               173
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     12
  LUNG CLEAR CELL ADENOCARCINOMA                                     0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 0
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     16
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      2
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  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     5 173
  8P LOSS WILD-TYPE  16 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5  173
  8P LOSS WILD-TYPE   16  268
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                5                16
  YES             173               268
[1] 2 2
[1] FALSE
D55V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   126   1   1  10
  8P LOSS WILD-TYPE 192  10   3   9
D55V12, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             126               192
  R1               1                10
  R2               1                 3
  RX              10                 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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1     4
  8P LOSS WILD-TYPE                                0     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                           8   136
  8P LOSS WILD-TYPE                        18   226
D55V13, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 2
  BLACK OR AFRICAN AMERICAN                      8                18
  WHITE                                        136               226
[1] 4 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     5 126
  8P LOSS WILD-TYPE   2 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5  126
  8P LOSS WILD-TYPE    2  206
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             126               206
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    35   8
  8Q LOSS WILD-TYPE 286  74
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               43               360 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8                74 
$`8Q LOSS MUTATED`
TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-44-2657 TCGA-44-6145 
        1997          912          365          669          400          328 
TCGA-44-6775 TCGA-44-7660 TCGA-49-4501 TCGA-49-6743 TCGA-49-6744 TCGA-50-5049 
         705          592         1421          369          890         2146 
TCGA-50-5068 TCGA-50-6597 TCGA-53-7626 TCGA-55-7573 TCGA-55-7727 TCGA-55-7903 
        1499         1015         1971            4           34           19 
TCGA-55-8506 TCGA-64-1676 TCGA-64-1679 TCGA-67-6217 TCGA-69-7980 TCGA-73-4662 
          11         1728         1686          422          382          912 
TCGA-73-4668 TCGA-73-7498 TCGA-75-7025 TCGA-78-7150 TCGA-78-8640 TCGA-86-6851 
         467          621         1967         1963         1949         1959 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8279 TCGA-95-7039 TCGA-95-7944 TCGA-97-7546 
          10           24          482           34          377          964 
TCGA-97-7554 TCGA-97-8171 TCGA-97-8547 TCGA-97-A4M7 TCGA-MN-A4N4 TCGA-MP-A4T7 
         775          107          148          271          622         1954 
TCGA-MP-A4TK 
        1971 

$`8Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4424 
        1431          578          610         1958          455          913 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         791          791          761          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         151          882          670           30           62           14 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
         225          182          264         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
        1492          864         1073          354         1357          448 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 
        1971          133         1324         1429         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1036          190          722         1013          863          383 
TCGA-44-6144 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
         723          302          845          704          658         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 
        1942         1864         1978          444          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         557         1970          882          535          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
          99          260          486          466          287          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 
         351          415           76         1932         1081          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         999          268          896          157         1700          445 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         522          354         2174          455          785          944 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         246          282          267         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 
         567          883          764          686          255          105 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
        1986          424          280          701         1178         1479 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
        1375           87            2          993           24         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
          25         1475           67         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 
        1170           18           35          121            6           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
          40         1958           39           39           24           54 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          16          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33           21          100            6           43           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           4           47           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
         216           44           23           29            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
          15           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          42           29           48         1952            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           5           47          162         1216         1289         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        2696         1445         2067         2199         1246          910 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
         628         1189         1126         1968         1959           62 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1305          864         1559          866           31          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
         573          427          385          174          141          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         186          690          414          165          230          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          70           89          100           77          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
          61         1600          711          800          131           40 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 
         164           38          519         1970         1956         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
        1973         1988         1950         1944         1093         1202 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
         760         1948         1957         1961         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          215         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1965         1972         1949         1944          327          881 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
        1952          994         1971         1981         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
        1965         1972          824           11          630          422 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
        1968          591         1963          508          745         1963 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 
          13          479          489          476           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          19           26           35           45           34           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
          15          455          405           10           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323         1940           60          310           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
         417          372          842          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
         127          186            2          568          477          476 
TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 
         121         1965         1932         1332          181           22 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
         182         1965           87          147           15          115 
TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         197          392          427          459           44          170 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
         154          114          287          282          238          578 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
         435          116            6          285          353         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1967         1951         1954         1957         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1944         1970         1970          142         1955         1490 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                 1 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             2146              2696 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              622               455 
[1] "4.0 - 2146.0 (622.0)" "1.0 - 2696.0 (455.0)"
[1] "hr=" "1.5"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  8Q LOSS MUTATED         1       12        9         9         7          7
  8Q LOSS WILD-TYPE       3      101      122        34        62         60
                   vv
clus                STAGE IIIB STAGE IV
  8Q LOSS MUTATED            2        3
  8Q LOSS WILD-TYPE          9       20
D56V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                12               101
  STAGE IB                 9               122
  STAGE IIA                9                34
  STAGE IIB                7                62
  STAGE IIIA               7                60
  STAGE IIIB               2                 9
  STAGE IV                 3                20
[1] 8 2
[1] 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    19  24   5   2
  8Q LOSS WILD-TYPE 124 235  35  16
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              19               124
  T2              24               235
  T3               5                35
  T4               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                 N0  N1 N2+N3
  8Q LOSS MUTATED    26  13    10
  8Q LOSS WILD-TYPE 269  72    62
D56V5, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0                 26               269
  N1                 13                72
  N2+N3              10                62
[1] 3 2
[1] 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 M1B  MX
  8Q LOSS MUTATED    34   2   1   0  13
  8Q LOSS WILD-TYPE 283  16   0   3 106
D56V6, multiclass
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               34               283
  M1                2                16
  M1A               1                 0
  M1B               0                 3
  MX               13               106
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    31  19
  8Q LOSS WILD-TYPE 217 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     31   19
  8Q LOSS WILD-TYPE  217  195
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              31               217
  MALE                19               195
[1] 2 2
[1] FALSE
D56V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8Q LOSS MUTATED                            1
  8Q LOSS WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8Q LOSS MUTATED                                   9
  8Q LOSS WILD-TYPE                                84
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                   32
  8Q LOSS WILD-TYPE                                                262
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8Q LOSS MUTATED                                            0
  8Q LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  8Q LOSS MUTATED                                               1
  8Q LOSS WILD-TYPE                                            18
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  8Q LOSS MUTATED                                1
  8Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  8Q LOSS MUTATED                                    3
  8Q LOSS WILD-TYPE                                  1
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  8Q LOSS MUTATED                              0                             2
  8Q LOSS WILD-TYPE                            2                            17
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  8Q LOSS MUTATED                                 0
  8Q LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  8Q LOSS MUTATED                                               1
  8Q LOSS WILD-TYPE                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  8Q LOSS MUTATED                              0
  8Q LOSS WILD-TYPE                            7
D56V9, multiclass
                                                    clus
vv                                                   8Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              32
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    1
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               3
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    2
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   8Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               262
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     18
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 1
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     17
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      3
  MUCINOUS (COLLOID) CARCINOMA                                       7
[1] 12  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  49
  8Q LOSS WILD-TYPE  20 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   49
  8Q LOSS WILD-TYPE   20  392
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                1                20
  YES              49               392
[1] 2 2
[1] FALSE
D56V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    35   1   0   1
  8Q LOSS WILD-TYPE 283  10   4  18
D56V12, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              35               283
  R1               1                10
  R2               0                 4
  RX               1                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  1     1
  8Q LOSS WILD-TYPE                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           1    36
  8Q LOSS WILD-TYPE                        25   326
D56V13, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                 5
  BLACK OR AFRICAN AMERICAN                      1                25
  WHITE                                         36               326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  35
  8Q LOSS WILD-TYPE   6 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   35
  8Q LOSS WILD-TYPE    6  297
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              35               297
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   159  52
  9P LOSS WILD-TYPE 162  30
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              211               192 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               52                30 
$`9P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4405 TCGA-05-4415 
        1523          426         1369         1947          610         1997 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
         912          913          730          457          151          882 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 
          30           62          225         1147         1492         1073 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 
         354         1357          448          133          400         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6146 
         741         1280         1013          863          723          302 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
        1942         1864         1978          592          218          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS 
        1970          882          535          385          260          415 
TCGA-44-A4SU TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
          76         1081         1421          428          999          896 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 
        1700          445          369          785         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5944 
         282          267         1091         2370          653          764 
TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
         686          255          105         1986         1971          424 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
         701         1178         1375           87          993           24 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 
          25           67         1233         2151           18           35 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 
           6            4           40         1958           39           16 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
           3           31          100            6           43           26 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8507 
           4           15           46           66           29            8 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48X TCGA-55-A490 
         228            3          536           15           33           48 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           1           28          162         1216         1289         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
        2696         1445         2199         1246          910         1728 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5815 TCGA-67-3770 
        1189         1686         1126         1968          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         610          573          385          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7974 TCGA-69-7980 TCGA-69-8255 
         186          690          414          184          382          129 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-75-6214 TCGA-75-7025 
         912          467          131           40         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1956         1965         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7166 
        1093         1963         1961          678          215         1934 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1937         1965          881         1952          994         1949 
TCGA-78-8655 TCGA-78-8660 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 
        1981         1954          630          422         1963          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
         745           10         1963           24          479          482 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8672 TCGA-86-A456 
          16           19           35           45           15           10 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
        1940           60          310           79          372          842 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8499 TCGA-93-7348 TCGA-95-7567 TCGA-95-7948 
         224           35           36          127          568          476 
TCGA-95-A4VK TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
         121          181         1965          147           15          148 
TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD 
         115          271           44          170          154          287 
TCGA-J2-A4AG TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         238          285          622          353         1946         1967 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1957         1980         1951         1970         1970 
TCGA-MP-A5C7 
        1490 

$`9P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4398 TCGA-05-4403 TCGA-05-4410 TCGA-05-4417 
         607         1126         1431          578         1958          455 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         365          669          791          791          761          761 
TCGA-05-5428 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
         670           14          182          264         1952         1962 
TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 TCGA-44-2656 TCGA-44-2665 TCGA-44-2666 
         864         1971         1324         1429         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         383          328          845          704          658          705 
TCGA-44-6776 TCGA-44-7659 TCGA-44-7661 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
        1938          444          366          719           99          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-49-4486 TCGA-49-4507 
         466          287          337          351         1932          268 
TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
         157          890          522          354         2174         2146 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5941 TCGA-50-5942 TCGA-50-6597 TCGA-53-A4EZ 
         455          944          567          883         1015          280 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 TCGA-55-6987 
        1479            2         1239         1475         1826         1170 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
         121           95           39           34           24           54 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          19          197           21            5           33           21 
TCGA-55-8096 TCGA-55-8205 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
          47           33          216           44           23           11 
TCGA-55-8508 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 TCGA-55-8619 
          15            9          146          202           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A494 
          66          106           42           29         1952            5 
TCGA-55-A4DF TCGA-62-A46U TCGA-64-1677 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
          47         2067          628         1959           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3773 TCGA-67-6215 TCGA-69-7765 TCGA-69-7973 
         864         1559          427          174          165          230 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 
          70           89          100           77          214           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
        1600          711          800          164           38          621 
TCGA-73-7499 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
         519         1202          760         1948         1957         1963 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        1221         1940         1950         1972         1949         1944 
TCGA-78-7539 TCGA-78-8648 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 
         327         1971         1964         1965         1972          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8073 TCGA-86-8076 
        1959           11         1968          591           13          489 
TCGA-86-8278 TCGA-86-8281 TCGA-86-8359 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
         476         1955           26           34           18          455 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6836 
         405           30           14           39          323          417 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         492          197          174           44          218          297 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-97-7546 
         186           34            2          377          477          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 
        1965         1932         1332          775           22          107 
TCGA-97-8172 TCGA-97-8175 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
         182           87          197          392          427          459 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         114          282          578          435          116            6 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1954         1944          142         1955         1971 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                 2 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             2696              2174 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            535.0             439.5 
[1] "1.0 - 2696.0 (535.0)" "2.0 - 2174.0 (439.5)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  9P LOSS MUTATED         3       53       62        26        38         39
  9P LOSS WILD-TYPE       1       60       69        17        31         28
                   vv
clus                STAGE IIIB STAGE IV
  9P LOSS MUTATED            6       13
  9P LOSS WILD-TYPE          5       10
D57V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  3                 1
  STAGE IA                53                60
  STAGE IB                62                69
  STAGE IIA               26                17
  STAGE IIB               38                31
  STAGE IIIA              39                28
  STAGE IIIB               6                 5
  STAGE IV                13                10
[1] 8 2
[1] 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    72 136  21  10
  9P LOSS WILD-TYPE  71 123  19   8
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              72                71
  T2             136               123
  T3              21                19
  T4              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                 N0  N1 N2+N3
  9P LOSS MUTATED   142  53    41
  9P LOSS WILD-TYPE 153  32    31
D57V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                142               153
  N1                 53                32
  N2+N3              41                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  9P LOSS MUTATED   168  11   0   2  57
  9P LOSS WILD-TYPE 149   7   1   1  62
D57V6, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              168               149
  M1               11                 7
  M1A               0                 1
  M1B               2                 1
  MX               57                62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   119 121
  9P LOSS WILD-TYPE 129  93
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    119  121
  9P LOSS WILD-TYPE  129   93
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE             119               129
  MALE               121                93
[1] 2 2
[1] FALSE
D57V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9P LOSS MUTATED                            7
  9P LOSS WILD-TYPE                          6
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9P LOSS MUTATED                                  48
  9P LOSS WILD-TYPE                                45
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                  155
  9P LOSS WILD-TYPE                                                139
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9P LOSS MUTATED                                            2
  9P LOSS WILD-TYPE                                          2
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  9P LOSS MUTATED                                              10
  9P LOSS WILD-TYPE                                             9
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  9P LOSS MUTATED                                1
  9P LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  9P LOSS MUTATED                                    4
  9P LOSS WILD-TYPE                                  0
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  9P LOSS MUTATED                              1                             7
  9P LOSS WILD-TYPE                            1                            12
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  9P LOSS MUTATED                                 0
  9P LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  9P LOSS MUTATED                                               3
  9P LOSS WILD-TYPE                                             1
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  9P LOSS MUTATED                              2
  9P LOSS WILD-TYPE                            5
D57V9, multiclass
                                                    clus
vv                                                   9P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             155
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               4
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                    7
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   9P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               139
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      9
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 0
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     12
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      1
  MUCINOUS (COLLOID) CARCINOMA                                       5
[1] 12  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    10 230
  9P LOSS WILD-TYPE  11 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     10  230
  9P LOSS WILD-TYPE   11  211
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               10                11
  YES             230               211
[1] 2 2
[1] FALSE
D57V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED   164   6   2  10
  9P LOSS WILD-TYPE 154   5   2   9
D57V12, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             164               154
  R1               6                 5
  R2               2                 2
  RX              10                 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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  1     2
  9P LOSS WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          13   190
  9P LOSS WILD-TYPE                        13   172
D57V13, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                     13                13
  WHITE                                        190               172
[1] 4 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     4 167
  9P LOSS WILD-TYPE   3 165
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4  167
  9P LOSS WILD-TYPE    3  165
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             167               165
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   153  44
  9Q LOSS WILD-TYPE 168  38
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              197               206 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               44                38 
$`9Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 
        1523          607         1369         1997          912          913 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5715 TCGA-35-4122 
         761          730          457          882           62          225 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 
         264         1952         1147         1492         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        1357          448          133          400         1367          741 
TCGA-44-2662 TCGA-44-5644 TCGA-44-6144 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 
        1280          863          723          658         1942         1864 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         592          218          557         1970          882          535 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 TCGA-49-4501 
         385          260          415           76         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
         428          999          896         1700          445          369 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
         785         1499          246          267         1091         2370 
TCGA-50-5935 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
         653          764          255          105         1986          424 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
         701         1178         1375           87          993           24 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 
          25           67         1233         2151           18           35 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7911 
           6            4         1958           39           16           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 
           3           31          100            6           26            4 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
          15           46           66           29            8           15 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48X 
         228            3          202          536           15           33 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
        1952            1           28            5           47          162 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-64-1676 
        1289         1970         2696         1445         2199         1728 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5779 TCGA-67-3770 
        1686         1126         1968         1959          864           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         610          573          385          422          202          186 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K 
         690          230          184          382          129          214 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-75-6214 
         711          912          467          131           40         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1967         1956         1973         1988         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 
        1093         1963         1221          215         1937         1965 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-86-7711 TCGA-86-7713 
         994         1949         1954         1972          630          422 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
        1963          508           10           24          479          482 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8672 TCGA-86-A456 
          16           19           35           45           15           10 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
        1940           60          310           79          372          842 
TCGA-91-6848 TCGA-91-8499 TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 
         224           36          127           34          568          476 
TCGA-95-A4VK TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
         121          181         1965          147          148          115 
TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG 
         271           44          170          154          287          238 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 
         285          622          353         1946         1967         1954 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 
        1980         1951         1970         1970         1490 

$`9Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
         426         1126         1947         1431          578          610 
TCGA-05-4410 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        1958          455          365          669          791          791 
TCGA-05-4430 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 
         761          151          670           30           14          182 
TCGA-38-4626 TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 TCGA-44-2656 TCGA-44-2665 
        1962          864         1971         1324         1429         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         722         1013          383          328          302          845 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 
         704          705         1938         1978          444          366 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
         719           99          486          466          287          337 
TCGA-44-A47G TCGA-49-4486 TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 
         351         1932          268          157          890          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5930 
         354         2174         2146          455          944          282 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6597 TCGA-53-7626 TCGA-53-A4EZ 
         567          883          686         1015         1971          280 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 TCGA-55-6987 
        1479            2         1239         1475         1826         1170 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
         121           95           40           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          54           19          197            5           33           21 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8205 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          43           47           33          216           44           23 
TCGA-55-8506 TCGA-55-8511 TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
          11            9          146           48           49           66 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-62-8395 TCGA-62-A46U 
         106           42           29           48         1216         2067 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-5775 TCGA-64-5778 
        1246          910          628         1189           62         1305 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7764 
        1559          866          427          174          141          414 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 
         165           70           89          100           77           61 
TCGA-73-4658 TCGA-73-4666 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        1600          800          164           38          621          519 
TCGA-75-7031 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1965         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
        1963          678         1940         1950         1934         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
        1949         1944          327          881         1952         1971 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1981         1964         1965          824         1959           11 
TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
        1968          591          745         1963           13          489 
TCGA-86-8278 TCGA-86-8281 TCGA-86-8359 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
         476         1955           26           34           18          455 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6836 
         405           30           14           39          323          417 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
          35          492          197          174           44          218 
TCGA-93-7347 TCGA-93-8067 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-97-7546 
         297          186            2          377          477          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 
        1965         1932         1332          775           22          107 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 
         182           87           15          197          392          427 
TCGA-99-8028 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         459          114          282          578          435          116 
TCGA-L9-A444 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TH 
           6         1951         1954         1957         1944          142 
TCGA-MP-A4TI TCGA-MP-A4TK 
        1955         1971 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 2 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             2696              2174 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              476               457 
[1] "1.0 - 2696.0 (476.0)" "2.0 - 2174.0 (457.0)"
[1] "hr=" "1"  
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  9Q LOSS MUTATED         3       54       61        24        32         36
  9Q LOSS WILD-TYPE       1       59       70        19        37         31
                   vv
clus                STAGE IIIB STAGE IV
  9Q LOSS MUTATED            4       12
  9Q LOSS WILD-TYPE          7       11
D58V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  3                 1
  STAGE IA                54                59
  STAGE IB                61                70
  STAGE IIA               24                19
  STAGE IIB               32                37
  STAGE IIIA              36                31
  STAGE IIIB               4                 7
  STAGE IV                12                11
[1] 8 2
[1] 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    73 128  19   5
  9Q LOSS WILD-TYPE  70 131  21  13
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              73                70
  T2             128               131
  T3              19                21
  T4               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                 N0  N1 N2+N3
  9Q LOSS MUTATED   137  46    38
  9Q LOSS WILD-TYPE 158  39    34
D58V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                137               158
  N1                 46                39
  N2+N3              38                34
[1] 3 2
[1] 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 M1B  MX
  9Q LOSS MUTATED   153  10   0   2  59
  9Q LOSS WILD-TYPE 164   8   1   1  60
D58V6, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              153               164
  M1               10                 8
  M1A               0                 1
  M1B               2                 1
  MX               59                60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   120 106
  9Q LOSS WILD-TYPE 128 108
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    120  106
  9Q LOSS WILD-TYPE  128  108
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE             120               128
  MALE               106               108
[1] 2 2
[1] FALSE
D58V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9Q LOSS MUTATED                            6
  9Q LOSS WILD-TYPE                          7
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9Q LOSS MUTATED                                  40
  9Q LOSS WILD-TYPE                                53
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                  150
  9Q LOSS WILD-TYPE                                                144
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9Q LOSS MUTATED                                            1
  9Q LOSS WILD-TYPE                                          3
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  9Q LOSS MUTATED                                              10
  9Q LOSS WILD-TYPE                                             9
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  9Q LOSS MUTATED                                1
  9Q LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  9Q LOSS MUTATED                                    4
  9Q LOSS WILD-TYPE                                  0
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  9Q LOSS MUTATED                              0                             7
  9Q LOSS WILD-TYPE                            2                            12
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  9Q LOSS MUTATED                                 1
  9Q LOSS WILD-TYPE                               0
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  9Q LOSS MUTATED                                               3
  9Q LOSS WILD-TYPE                                             1
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  9Q LOSS MUTATED                              3
  9Q LOSS WILD-TYPE                            4
D58V9, multiclass
                                                    clus
vv                                                   9Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             150
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                   10
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               4
  LUNG MUCINOUS ADENOCARCINOMA                                     0
  LUNG PAPILLARY ADENOCARCINOMA                                    7
  LUNG SIGNET RING ADENOCARCINOMA                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    3
  MUCINOUS (COLLOID) CARCINOMA                                     3
                                                    clus
vv                                                   9Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               144
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      9
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 0
  LUNG MUCINOUS ADENOCARCINOMA                                       2
  LUNG PAPILLARY ADENOCARCINOMA                                     12
  LUNG SIGNET RING ADENOCARCINOMA                                    0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      1
  MUCINOUS (COLLOID) CARCINOMA                                       4
[1] 12  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     9 217
  9Q LOSS WILD-TYPE  12 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9  217
  9Q LOSS WILD-TYPE   12  224
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                9                12
  YES             217               224
[1] 2 2
[1] FALSE
D58V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED   156   6   2  10
  9Q LOSS WILD-TYPE 162   5   2   9
D58V12, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0             156               162
  R1               6                 5
  R2               2                 2
  RX              10                 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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  1     2
  9Q LOSS WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          13   180
  9Q LOSS WILD-TYPE                        13   182
D58V13, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                     13                13
  WHITE                                        180               182
[1] 4 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     4 163
  9Q LOSS WILD-TYPE   3 169
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4  163
  9Q LOSS WILD-TYPE    3  169
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             163               169
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    61  21
  10P LOSS WILD-TYPE 260  61
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                82                321 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                21                 61 
$`10P LOSS MUTATED`
TCGA-05-5429 TCGA-05-5715 TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 TCGA-38-6178 
          30           62         1147         1492          354          448 
TCGA-44-2657 TCGA-44-2662 TCGA-44-3398 TCGA-44-3919 TCGA-44-6775 TCGA-44-6779 
         400         1280         1163          190          705         1978 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-A4SU TCGA-49-4494 
         592          218         1970          882           76         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-6742 TCGA-50-5931 TCGA-50-5944 TCGA-50-6597 
        1421          428          445          267          764         1015 
TCGA-55-1596 TCGA-55-6980 TCGA-55-6986 TCGA-55-7281 TCGA-55-7994 TCGA-55-8091 
        1375           67         2151           18           31           43 
TCGA-55-8094 TCGA-55-8514 TCGA-55-8614 TCGA-55-A48X TCGA-55-A4DF TCGA-55-A4DG 
           4          202          536           33           47          162 
TCGA-62-8402 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
        1445         1728         1686         1968         1959           62 
TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 TCGA-69-7973 TCGA-69-A59K TCGA-73-4659 
         864           31          573          230          214          711 
TCGA-73-4666 TCGA-73-4668 TCGA-78-7147 TCGA-78-7540 TCGA-78-8640 TCGA-78-8655 
         800          467         1950          881         1949         1981 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
        1954          824         1959         1963          745           10 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8669 
          24          479          476           16           26           34 
TCGA-91-6828 TCGA-91-6835 TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 TCGA-95-7043 
         323           79          372           36          127            2 
TCGA-95-7947 TCGA-97-7546 TCGA-97-8547 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AD 
         477          964          148          271          154          287 
TCGA-J2-A4AG TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 
         238         1951         1954         1980 

$`10P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
         761          761          730          457          151          882 
TCGA-05-5428 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
         670           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
        1962          864         1073         1357         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 
        1324         1429         1367          741         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
         246         1130         1036          722         1013          863 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
         383          723          328          302          845          704 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7661 
         658         1938         1942         1864          444          366 
TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         557          535          719          385           99          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         486          466          287          337          351          415 
TCGA-49-4486 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
        1932          999          268          896          157         1700 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
         369          890          522          354         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         455          785          944         1499          246          282 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
        1091         2370          653          567          883          686 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
         255          105         1986         1971          424          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         701         1178         1479           87            2          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 
          24         1239           25         1475         1826         1233 
TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        1170           35          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40         1958           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          54           19           16          197           21            3 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 
           5           33           21          100            6           26 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
          47           15           33           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          44           23           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 
         228            9            3          146           15           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          49           66          106           42           29           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 
        1952            1           28            5         1216         1289 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1970         2696         2067         2199         1246          910 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 
         628         1189         1126         1305         1559          866 
TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         610          427          385          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
         202          186          690          414          165          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
          70           89          382          100           77          129 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
          61         1600          912          131           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
          38          621          519         1970         1967         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1965         1973         1988         1944         1093         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1202          760         1948         1957         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1221          678          215         1940         1950         1934 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1937         1965         1972         1949         1944          327 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1952          994         1971         1964         1965         1972 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
          11          630          422         1968          591          508 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 
        1963           13          489          482         1955           19 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          35           45           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
          10           30           14           39         1940           60 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
         310          417          842          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 
         197          174           44          218          297          186 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 
          34          568          377          476          121         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
        1932         1332          775          181           22          107 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
         182         1965           87          147           15          115 
TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         197          392          427          459           44          170 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         114          282          578          435          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 
         285          622          353         1946         1967         1954 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1957         1951         1944         1970         1970          142 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                  1 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              2151               2696 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             471.5              459.0 
[1] "2.0 - 2151.0 (471.5)" "1.0 - 2696.0 (459.0)"
[1] "hr=" "1.4"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  10P LOSS MUTATED         0       28       23        11        17         16
  10P LOSS WILD-TYPE       4       85      108        32        52         51
                    vv
clus                 STAGE IIIB STAGE IV
  10P LOSS MUTATED            1        5
  10P LOSS WILD-TYPE         10       18
D59V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                 28                 85
  STAGE IB                 23                108
  STAGE IIA                11                 32
  STAGE IIB                17                 52
  STAGE IIIA               16                 51
  STAGE IIIB                1                 10
  STAGE IV                  5                 18
[1] 8 2
[1] 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    39  51   8   2
  10P LOSS WILD-TYPE 104 208  32  16
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               39                104
  T2               51                208
  T3                8                 32
  T4                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                  N0  N1 N2+N3
  10P LOSS MUTATED    59  23    17
  10P LOSS WILD-TYPE 236  62    55
D59V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                  59                236
  N1                  23                 62
  N2+N3               17                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  10P LOSS MUTATED    71   4   0   1  24
  10P LOSS WILD-TYPE 246  14   1   2  95
D59V6, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                71                246
  M1                 4                 14
  M1A                0                  1
  M1B                1                  2
  MX                24                 95
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    66  35
  10P LOSS WILD-TYPE 182 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     66   35
  10P LOSS WILD-TYPE  182  179
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               66                182
  MALE                 35                179
[1] 2 2
[1] FALSE
D59V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10P LOSS MUTATED                            4
  10P LOSS WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10P LOSS MUTATED                                  13
  10P LOSS WILD-TYPE                                80
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                   73
  10P LOSS WILD-TYPE                                                221
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10P LOSS MUTATED                                            1
  10P LOSS WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  10P LOSS MUTATED                                               4
  10P LOSS WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  10P LOSS MUTATED                                0
  10P LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  10P LOSS MUTATED                                    3
  10P LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  10P LOSS MUTATED                              0                             0
  10P LOSS WILD-TYPE                            2                            19
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  10P LOSS MUTATED                                 1
  10P LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  10P LOSS MUTATED                                               1
  10P LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  10P LOSS MUTATED                              1
  10P LOSS WILD-TYPE                            6
D59V9, multiclass
                                                    clus
vv                                                   10P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                13
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               73
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   10P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                221
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      19
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     2  99
  10P LOSS WILD-TYPE  19 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   99
  10P LOSS WILD-TYPE   19  342
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 2                 19
  YES               99                342
[1] 2 2
[1] FALSE
D59V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    78   1   1   4
  10P LOSS WILD-TYPE 240  10   3  15
D59V12, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               78                240
  R1                1                 10
  R2                1                  3
  RX                4                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  1     1
  10P LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           3    83
  10P LOSS WILD-TYPE                        23   279
D59V13, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       3                 23
  WHITE                                          83                279
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2  76
  10P LOSS WILD-TYPE   5 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   76
  10P LOSS WILD-TYPE    5  256
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               76                256
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    77  23
  10Q LOSS WILD-TYPE 244  59
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               100                303 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                23                 59 
$`10Q LOSS MUTATED`
TCGA-05-4410 TCGA-05-4420 TCGA-05-4424 TCGA-05-5429 TCGA-05-5715 TCGA-38-4627 
        1958          912          913           30           62         1147 
TCGA-38-4628 TCGA-38-4631 TCGA-44-2657 TCGA-44-2662 TCGA-44-3396 TCGA-44-3398 
        1492          354          400         1280         1130         1163 
TCGA-44-3919 TCGA-44-6775 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 
         190          705         1978          592          218         1970 
TCGA-44-7670 TCGA-44-A4SU TCGA-49-4494 TCGA-49-4505 TCGA-49-6742 TCGA-50-5931 
         882           76         1081          428          445          267 
TCGA-50-5944 TCGA-50-6597 TCGA-55-1596 TCGA-55-5899 TCGA-55-6971 TCGA-55-6980 
         764         1015         1375           87           25           67 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7994 TCGA-55-8091 TCGA-55-8206 TCGA-55-8207 
        2151           18           31           43           46           66 
TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-A48X TCGA-55-A4DF 
          29           15          202          536           33           47 
TCGA-55-A4DG TCGA-62-8402 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
         162         1445         1728         1686         1968         1959 
TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 TCGA-69-7973 TCGA-69-7978 
          62          864           31          573          230           70 
TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4668 TCGA-78-7147 
          89          129          214          800          467         1950 
TCGA-78-7535 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 
        1972          881         1952         1949         1981         1954 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 
         824         1959         1963          508           10           24 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8669 TCGA-91-6828 
         479          476           16           26           34          323 
TCGA-91-6829 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 TCGA-93-7348 
        1940           79          372          842           36          127 
TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-8175 
           2          377          477          476          964           87 
TCGA-97-8547 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A443 
         148          271          154          287          238          116 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TF 
        1951         1954         1980         1970 

$`10Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
        1431          578          610         1997          455          365 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         669          791          791          761          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-3615 TCGA-35-4122 
         457          151          882          670           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 TCGA-38-4630 
         182          264         1952         1962          864         1073 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1357          448         1971          133         1324         1429 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3918 
        1367          741         1301           97          246         1036 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
         722         1013          863          383          723          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 
         302          845          704          658         1938         1942 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7661 TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 
        1864          444          366          557          535          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
         385           99          260          486          466          287 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4501 TCGA-49-4506 
         337          351          415         1932         1421          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
         268          896          157         1700          369          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         522          354         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
         944         1499          246          282         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 
         653          567          883          686          255          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
        1986         1971          424          280          701         1178 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 
        1479            2          993           24         1239         1475 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        1826         1233         1170           35          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40         1958           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
          34           24           54           19           16          197 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
          21            3            5           33           21          100 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
           6           26            4           47           15           33 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
         216           44           23           11            8          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
           9            3          146           15           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
          66          106           42           29           48         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
           1           28            5         1216         1289         1970 
TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
        2696         2067         2199         1246          910          628 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        1189         1126         1305         1559          866          610 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         427          385          174          141          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7980 
         186          690          414          165          184          382 
TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
         100           77           61         1600          711          912 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         131           40          164           38          621          519 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
        1970         1967         1956         1965         1973         1988 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1944         1093         1963         1202          760         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1957         1961         1963         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        1940         1950         1934         1937         1965         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8648 TCGA-78-8662 TCGA-80-5607 
        1944          327          994         1971         1964         1965 
TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        1972           11          630          422         1968          591 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 TCGA-86-8281 
         745         1963           13          489          482         1955 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          19           35           45           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 
         405           10           30           14           39           60 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         310          417          224           35          492          197 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 
         174           44          218          297          186           34 
TCGA-95-7567 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         568          121         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 
         181           22          107          182         1965          147 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
          15          115          197          392          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
          44          170          114          282          578          435 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
           6          285          622          353         1946         1967 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH 
        1954         1957         1951         1944         1970          142 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                  1 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              2151               2696 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               456                466 
[1] "2.0 - 2151.0 (456.0)" "1.0 - 2696.0 (466.0)"
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  10Q LOSS MUTATED         0       33       35        13        20         15
  10Q LOSS WILD-TYPE       4       80       96        30        49         52
                    vv
clus                 STAGE IIIB STAGE IV
  10Q LOSS MUTATED            1        4
  10Q LOSS WILD-TYPE         10       19
D60V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                 33                 80
  STAGE IB                 35                 96
  STAGE IIA                13                 30
  STAGE IIB                20                 49
  STAGE IIIA               15                 52
  STAGE IIIB                1                 10
  STAGE IV                  4                 19
[1] 8 2
[1] 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    44  66   8   2
  10Q LOSS WILD-TYPE  99 193  32  16
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               44                 99
  T2               66                193
  T3                8                 32
  T4                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                  N0  N1 N2+N3
  10Q LOSS MUTATED    75  28    16
  10Q LOSS WILD-TYPE 220  57    56
D60V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                  75                220
  N1                  28                 57
  N2+N3               16                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  10Q LOSS MUTATED    86   4   0   0  31
  10Q LOSS WILD-TYPE 231  14   1   3  88
D60V6, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                86                231
  M1                 4                 14
  M1A                0                  1
  M1B                0                  3
  MX                31                 88
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    73  48
  10Q LOSS WILD-TYPE 175 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     73   48
  10Q LOSS WILD-TYPE  175  166
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               73                175
  MALE                 48                166
[1] 2 2
[1] FALSE
D60V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10Q LOSS MUTATED                            5
  10Q LOSS WILD-TYPE                          8
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10Q LOSS MUTATED                                  18
  10Q LOSS WILD-TYPE                                75
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                   83
  10Q LOSS WILD-TYPE                                                211
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10Q LOSS MUTATED                                            1
  10Q LOSS WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  10Q LOSS MUTATED                                               5
  10Q LOSS WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  10Q LOSS MUTATED                                0
  10Q LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  10Q LOSS MUTATED                                    3
  10Q LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  10Q LOSS MUTATED                              0                             0
  10Q LOSS WILD-TYPE                            2                            19
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  10Q LOSS MUTATED                                 1
  10Q LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  10Q LOSS MUTATED                                               3
  10Q LOSS WILD-TYPE                                             1
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  10Q LOSS MUTATED                              2
  10Q LOSS WILD-TYPE                            5
D60V9, multiclass
                                                    clus
vv                                                   10Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               83
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   10Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  75
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                211
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      19
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       1
  MUCINOUS (COLLOID) CARCINOMA                                        5
[1] 12  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     2 119
  10Q LOSS WILD-TYPE  19 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2  119
  10Q LOSS WILD-TYPE   19  322
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 2                 19
  YES              119                322
[1] 2 2
[1] FALSE
D60V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    89   1   1   6
  10Q LOSS WILD-TYPE 229  10   3  13
D60V12, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               89                229
  R1                1                 10
  R2                1                  3
  RX                6                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  1     1
  10Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           4    97
  10Q LOSS WILD-TYPE                        22   265
D60V13, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       4                 22
  WHITE                                          97                265
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3  86
  10Q LOSS WILD-TYPE   4 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3   86
  10Q LOSS WILD-TYPE    4  246
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               86                246
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    72  19
  11P LOSS WILD-TYPE 249  63
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                91                312 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                19                 63 
$`11P LOSS MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4410 TCGA-05-4427 TCGA-05-4433 
         607         1369         1126         1958          791          730 
TCGA-05-5425 TCGA-05-5428 TCGA-35-5375 TCGA-38-4625 TCGA-38-4632 TCGA-44-2662 
         882          670          264         1952         1357         1280 
TCGA-44-3918 TCGA-44-5643 TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 TCGA-44-A47F 
        1036         1013          218          557          535          337 
TCGA-44-A4SS TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-50-5072 
         415          428          999          268          896          246 
TCGA-50-5931 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-1596 
         267         1986         1971          280         1479         1375 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6972 TCGA-55-7570 TCGA-55-7573 TCGA-55-7727 
          87          993         1475            6            4           34 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7994 TCGA-55-8089 TCGA-55-8302 TCGA-55-8507 
          54           19           31          100           23            8 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8615 TCGA-55-A490 TCGA-55-A492 TCGA-55-A4DG 
         228            9           15           48            1          162 
TCGA-62-8397 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-5774 
        1289         1246          910         1728         1686         1959 
TCGA-64-5778 TCGA-64-5815 TCGA-69-7763 TCGA-69-7764 TCGA-69-A59K TCGA-73-4659 
        1305          866          690          414          214          711 
TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-75-7025 TCGA-78-7145 TCGA-78-7148 
         131           40          519         1967         1973         1944 
TCGA-78-7154 TCGA-78-7160 TCGA-78-7535 TCGA-78-8640 TCGA-86-7701 TCGA-86-7711 
        1948          678         1972         1949           11          630 
TCGA-86-7713 TCGA-86-7953 TCGA-86-8074 TCGA-86-8358 TCGA-86-8669 TCGA-86-A4D0 
         422          591           24           19           34           30 
TCGA-91-6836 TCGA-91-6847 TCGA-93-8067 TCGA-95-7948 TCGA-97-7553 TCGA-97-8174 
         417          842          186          476         1332         1965 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-MN-A4N1 TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TE 
         287          578          285         1951         1957         1970 
TCGA-MP-A4TF 
        1970 

$`11P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        1523          426         1947         1431          578          610 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        1997          455          912          365          913          669 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 
         791          761          761          457          151           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 
          62           14          225          182         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
        1492          864         1073          354          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
        1301           97          246         1130         1163          190 
TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
         722          863          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7669 
        1864         1978          444          592          366         1970 
TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         882          719          385           99          260          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         466          287          351           76         1932         1081 
TCGA-49-4501 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
        1421          157         1700          445          369          890 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         522          354         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
         944         1499          282         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 
         567          883          764          686         1015          255 
TCGA-50-8460 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 
         105          424          701         1178            2           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        1239           25           67         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 TCGA-55-7576 
        1170           18           35          121           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 
        1958           39           39           24           16          197 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
          21            3            5           33           21            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
          43           26            4           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
          46           66          216           44           29           11 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
          15            3          146          202          536           48 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
          49           66          106           33           42           29 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8398 
        1952           28            5           47         1216         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-64-1677 TCGA-64-1678 
        2696         1445         2067         2199          628         1189 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 
        1126         1968           62          864         1559           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         610          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         422          202          186          165          230          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
          70           89          382          100           77          129 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 
          61         1600          912          800          467          164 
TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
          38          621         1970         1956         1965         1988 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        1950         1093         1963         1202          760         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1961         1963         1221          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1965         1949         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
         881         1952          994         1971         1981         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7714 
        1964         1965         1972          824         1959         1968 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
        1963          508          745           10         1963           13 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
         479          489          476          482           16         1955 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          26           35           45           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
         405           10           14           39          323         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 
          60          310           79          372          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          197          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
         297          127           34            2          568          377 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 
         477          121          964         1965         1932          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 
         181           22          107          182           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
          15          148          115          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         427          459           44          170          154          114 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 
         282          238          435          116            6          622 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
         353         1946         1967         1954         1954         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1944          142         1955         1971         1490 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  2 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1986               2696 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             607.0              446.5 
[1] "1.0 - 1986.0 (607.0)" "2.0 - 2696.0 (446.5)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  11P LOSS MUTATED         1       22       28        13        18         15
  11P LOSS WILD-TYPE       3       91      103        30        51         52
                    vv
clus                 STAGE IIIB STAGE IV
  11P LOSS MUTATED            0        7
  11P LOSS WILD-TYPE         11       16
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 22                 91
  STAGE IB                 28                103
  STAGE IIA                13                 30
  STAGE IIB                18                 51
  STAGE IIIA               15                 52
  STAGE IIIB                0                 11
  STAGE IV                  7                 16
[1] 8 2
[1] 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    30  58  13   3
  11P LOSS WILD-TYPE 113 201  27  15
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               30                113
  T2               58                201
  T3               13                 27
  T4                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                  N0  N1 N2+N3
  11P LOSS MUTATED    66  24    14
  11P LOSS WILD-TYPE 229  61    58
D61V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                  66                229
  N1                  24                 61
  N2+N3               14                 58
[1] 3 2
[1] 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 M1B  MX
  11P LOSS MUTATED    72   7   0   0  25
  11P LOSS WILD-TYPE 245  11   1   3  94
D61V6, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                72                245
  M1                 7                 11
  M1A                0                  1
  M1B                0                  3
  MX                25                 94
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    40  64
  11P LOSS WILD-TYPE 208 150
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     40   64
  11P LOSS WILD-TYPE  208  150
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               40                208
  MALE                 64                150
[1] 2 2
[1] FALSE
D61V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11P LOSS MUTATED                            1
  11P LOSS WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11P LOSS MUTATED                                  21
  11P LOSS WILD-TYPE                                72
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                   75
  11P LOSS WILD-TYPE                                                219
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11P LOSS MUTATED                                            0
  11P LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  11P LOSS MUTATED                                               2
  11P LOSS WILD-TYPE                                            17
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  11P LOSS MUTATED                                1
  11P LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  11P LOSS MUTATED                                    0
  11P LOSS WILD-TYPE                                  4
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  11P LOSS MUTATED                              0                             3
  11P LOSS WILD-TYPE                            2                            16
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  11P LOSS MUTATED                                 0
  11P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  11P LOSS MUTATED                                               0
  11P LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  11P LOSS MUTATED                              1
  11P LOSS WILD-TYPE                            6
D61V9, multiclass
                                                    clus
vv                                                   11P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               75
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   11P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  72
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                219
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      17
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  4
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      16
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     3 101
  11P LOSS WILD-TYPE  18 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3  101
  11P LOSS WILD-TYPE   18  340
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 3                 18
  YES              101                340
[1] 2 2
[1] FALSE
D61V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    73   2   1   7
  11P LOSS WILD-TYPE 245   9   3  12
D61V12, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               73                245
  R1                2                  9
  R2                1                  3
  RX                7                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     3
  11P LOSS WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           8    79
  11P LOSS WILD-TYPE                        18   283
D61V13, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  3
  BLACK OR AFRICAN AMERICAN                       8                 18
  WHITE                                          79                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"
D61V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     3  78
  11P LOSS WILD-TYPE   4 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3   78
  11P LOSS WILD-TYPE    4  254
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               78                254
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    59  14
  11Q LOSS WILD-TYPE 262  68
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                73                330 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                14                 68 
$`11Q LOSS MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 
         607         1369         1126          791          730          457 
TCGA-05-5425 TCGA-05-5428 TCGA-35-5375 TCGA-38-4625 TCGA-38-4631 TCGA-44-3918 
         882          670          264         1952          354         1036 
TCGA-44-4112 TCGA-44-5643 TCGA-44-7667 TCGA-44-7671 TCGA-44-A47F TCGA-44-A4SS 
         722         1013          557          535          337          415 
TCGA-49-4506 TCGA-49-4510 TCGA-50-5072 TCGA-50-5931 TCGA-53-7626 TCGA-55-1595 
         999          896          246          267         1971         1479 
TCGA-55-6972 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7995 TCGA-55-8089 
        1475           34           54           19            5          100 
TCGA-55-8094 TCGA-55-8302 TCGA-55-8507 TCGA-55-8511 TCGA-55-8615 TCGA-55-A490 
           4           23            8            9           15           48 
TCGA-62-8397 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-5774 
        1289          910         1728         1189         1686         1959 
TCGA-64-5778 TCGA-64-5815 TCGA-69-7763 TCGA-69-7764 TCGA-73-4662 TCGA-73-4675 
        1305          866          690          414          912           40 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7148 TCGA-78-7160 
         519         1970         1967         1973         1944          678 
TCGA-78-8640 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8074 
        1949           11          422          591          745           24 
TCGA-86-8358 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6847 TCGA-93-8067 TCGA-97-8174 
          19           34           30          842          186         1965 
TCGA-J2-A4AD TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TE 
         287          285          353         1951         1957         1970 
TCGA-MP-A4TF 
        1970 

$`11Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        1523          426         1947         1431          578          610 
TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        1958         1997          455          912          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5429 
         669          791          761          761          151           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 
          62           14          225          182         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
        1492          864         1073         1357          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3919 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
         190          863          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
        1864         1978          444          592          366          218 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
        1970          882          719          385           99          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 
         486          466          287          351           76         1932 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
        1081         1421          428          268          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
         445          369          890          522          354         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
        2146          455          785          944         1499          282 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
         686         1015          255          105         1986          424 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
         280          701         1178         1375           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 
         993           24         1239           25           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1233         2151         1170           18           35          121 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
           6            4           95           40         1958           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          39           24           16          197           21            3 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          31           33           21            6           43           26 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
          47           15           33           46           66          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
          44           29           11           15          228            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         146          202          536           48           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
         106           33           42           29         1952            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 
          28            5           47          162         1216         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-64-1677 
        2696         1445         2067         2199         1246          628 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 
        1126         1968           62          864         1559           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         610          573          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         422          202          186          165          230          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
          70           89          382          100           77          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
         214           61         1600          711          800          467 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 TCGA-75-7031 
         131          164           38          621         1956         1965 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1988         1950         1093         1963         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 
        1948         1957         1961         1963         1221          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        1940         1950         1934         1937         1965         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1949         1944          327          881         1952          994 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1971         1981         1954         1964         1965         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
         824         1959          630         1968         1963          508 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
          10         1963           13          479          489          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
         482           16         1955           26           35           45 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
          18           15          455          405           10           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323         1940           60          310           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         417          372          224           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         174           36           44          218          297          127 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
          34            2          568          377          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         121          964         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 
         181           22          107          182           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
          15          148          115          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         427          459           44          170          154          114 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         282          238          578          435          116            6 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
         622         1946         1967         1954         1954         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1951         1944          142         1955         1971         1490 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                  1 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              1973               2696 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             678.0              444.5 
[1] "4.0 - 1973.0 (678.0)" "1.0 - 2696.0 (444.5)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  11Q LOSS MUTATED         0       19       22        12        13         13
  11Q LOSS WILD-TYPE       4       94      109        31        56         54
                    vv
clus                 STAGE IIIB STAGE IV
  11Q LOSS MUTATED            0        4
  11Q LOSS WILD-TYPE         11       19
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                 19                 94
  STAGE IB                 22                109
  STAGE IIA                12                 31
  STAGE IIB                13                 56
  STAGE IIIA               13                 54
  STAGE IIIB                0                 11
  STAGE IV                  4                 19
[1] 8 2
[1] 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    26  47   8   2
  11Q LOSS WILD-TYPE 117 212  32  16
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               26                117
  T2               47                212
  T3                8                 32
  T4                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                  N0  N1 N2+N3
  11Q LOSS MUTATED    55  15    13
  11Q LOSS WILD-TYPE 240  70    59
D62V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                  55                240
  N1                  15                 70
  N2+N3               13                 59
[1] 3 2
[1] 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 M1B  MX
  11Q LOSS MUTATED    65   3   0   1  14
  11Q LOSS WILD-TYPE 252  15   1   2 105
D62V6, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                65                252
  M1                 3                 15
  M1A                0                  1
  M1B                1                  2
  MX                14                105
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    32  51
  11Q LOSS WILD-TYPE 216 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     32   51
  11Q LOSS WILD-TYPE  216  163
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               32                216
  MALE                 51                163
[1] 2 2
[1] FALSE
D62V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11Q LOSS MUTATED                            2
  11Q LOSS WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11Q LOSS MUTATED                                  16
  11Q LOSS WILD-TYPE                                77
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                   59
  11Q LOSS WILD-TYPE                                                235
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11Q LOSS MUTATED                                            0
  11Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  11Q LOSS MUTATED                                               1
  11Q LOSS WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  11Q LOSS MUTATED                                1
  11Q LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  11Q LOSS MUTATED                                    0
  11Q LOSS WILD-TYPE                                  4
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  11Q LOSS MUTATED                              0                             3
  11Q LOSS WILD-TYPE                            2                            16
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  11Q LOSS MUTATED                                 0
  11Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  11Q LOSS MUTATED                                               0
  11Q LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  11Q LOSS MUTATED                              1
  11Q LOSS WILD-TYPE                            6
D62V9, multiclass
                                                    clus
vv                                                   11Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                16
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               59
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   11Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                235
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  4
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      16
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     2  81
  11Q LOSS WILD-TYPE  19 360
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   81
  11Q LOSS WILD-TYPE   19  360
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 2                 19
  YES               81                360
[1] 2 2
[1] FALSE
D62V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    62   2   0   5
  11Q LOSS WILD-TYPE 256   9   4  14
D62V12, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               62                256
  R1                2                  9
  R2                0                  4
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           5    63
  11Q LOSS WILD-TYPE                        21   299
D62V13, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       5                 21
  WHITE                                          63                299
[1] 4 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     0  64
  11Q LOSS WILD-TYPE   7 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   64
  11Q LOSS WILD-TYPE    7  268
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               64                268
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    68  14
  12P LOSS WILD-TYPE 253  68
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                82                321 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                14                 68 
$`12P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4405 TCGA-05-4426 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 
        1523          610          791          448         1429          400 
TCGA-44-2661 TCGA-44-2666 TCGA-44-6775 TCGA-44-6779 TCGA-44-7662 TCGA-44-7671 
         741           97          705         1978          218          535 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SU TCGA-49-4501 
         385          260          287          337           76         1421 
TCGA-49-4510 TCGA-49-6743 TCGA-49-6744 TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 
         896          369          890         2146          455         1499 
TCGA-50-5932 TCGA-50-5942 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-5899 
        1091          883          686         1015          701           87 
TCGA-55-7573 TCGA-55-7727 TCGA-55-7914 TCGA-55-8087 TCGA-55-8510 TCGA-55-8511 
           4           34            3           21          228            9 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-A48X TCGA-55-A48Z 
         202          536           48           49           33           29 
TCGA-55-A491 TCGA-55-A4DG TCGA-64-1676 TCGA-64-5778 TCGA-67-3771 TCGA-67-6217 
        1952          162         1728         1305          610          422 
TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-8253 TCGA-71-6725 TCGA-73-4677 
         690          165          184          100           61           38 
TCGA-73-7498 TCGA-75-6214 TCGA-78-7147 TCGA-78-7153 TCGA-78-7535 TCGA-86-7701 
         621         1970         1950          760         1972           11 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8672 
          13           24          479          482           19           15 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-95-7039 TCGA-95-7043 TCGA-95-7947 
         842           35          492           34            2          477 
TCGA-95-7948 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-8177 TCGA-99-7458 
         476          964         1965          775          147          392 
TCGA-99-8025 TCGA-J2-A4AD TCGA-MP-A4TC TCGA-MP-A4TK 
         427          287         1944         1971 

$`12P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
         607          426         1369         1126         1947         1431 
TCGA-05-4403 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
         578         1958         1997          455          912          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         913          669          791          761          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
         457          151          882          670           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
          14          225          182          264         1952         1962 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
        1147         1492          864         1073          354         1357 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 
        1971          133         1324         1367         1280         1301 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1013          863          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         845          704          658         1938         1942         1864 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         444          592          366          557         1970          882 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS 
         719           99          486          466          351          415 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 
        1932         1081          428          999          268          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5055 
        1700          445          522          354         2174          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
         944          246          282          267         2370          653 
TCGA-50-5941 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         567          764          255          105         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 
         424          280         1178         1479         1375            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
         993           24         1239           25         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1826         1233         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
         121            6           95           40         1958           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
          39           24           54           19           16          197 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 
          21           31            5           33          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
          43           26            4           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          46           66          216           44           23           29 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
          11            8           15            3          146           15 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 
          66          106           42           48            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
           5           47         1216         1289         1970         2696 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
        1445         2067         2199         1246          910          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
        1189         1686         1126         1968         1959           62 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
         864         1559          866           31          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
         385          174          141          202          186          414 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 
         230           70           89          382           77          129 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
         214         1600          711          912          800          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-7025 TCGA-75-7027 
         131           40          164          519         1967         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1965         1973         1988         1944         1093         1963 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1202         1948         1957         1961         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          215         1940         1950         1934         1937 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1965         1949         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
         994         1949         1971         1981         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
        1965         1972          824         1959          630          422 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
        1968          591         1963          508          745           10 
TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 
        1963          489          476           16         1955           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
          35           45           34           18          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
          10           30           14           39          323         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 
          60          310           79          417          372          224 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VK TCGA-97-7552 
         127          186          568          377          121         1932 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        1332          181           22          107          182         1965 
TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
          87           15          148          115          197          271 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
         459           44          170          154          114          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         238          578          435          116            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         622          353         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1957         1980         1951         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
         142         1955         1490 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                  1 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              2146               2696 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             451.5              467.0 
[1] "2.0 - 2146.0 (451.5)" "1.0 - 2696.0 (467.0)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  12P LOSS MUTATED         0       21       37         6        15         14
  12P LOSS WILD-TYPE       4       92       94        37        54         53
                    vv
clus                 STAGE IIIB STAGE IV
  12P LOSS MUTATED            1        4
  12P LOSS WILD-TYPE         10       19
D63V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                 21                 92
  STAGE IB                 37                 94
  STAGE IIA                 6                 37
  STAGE IIB                15                 54
  STAGE IIIA               14                 53
  STAGE IIIB                1                 10
  STAGE IV                  4                 19
[1] 8 2
[1] 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    26  61   7   3
  12P LOSS WILD-TYPE 117 198  33  15
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               26                117
  T2               61                198
  T3                7                 33
  T4                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                  N0  N1 N2+N3
  12P LOSS MUTATED    64  19    14
  12P LOSS WILD-TYPE 231  66    58
D63V5, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                  64                231
  N1                  19                 66
  N2+N3               14                 58
[1] 3 2
[1] 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 M1B  MX
  12P LOSS MUTATED    59   3   0   0  35
  12P LOSS WILD-TYPE 258  15   1   3  84
D63V6, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                59                258
  M1                 3                 15
  M1A                0                  1
  M1B                0                  3
  MX                35                 84
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    63  35
  12P LOSS WILD-TYPE 185 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     63   35
  12P LOSS WILD-TYPE  185  179
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               63                185
  MALE                 35                179
[1] 2 2
[1] FALSE
D63V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12P LOSS MUTATED                            1
  12P LOSS WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12P LOSS MUTATED                                  20
  12P LOSS WILD-TYPE                                73
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                   65
  12P LOSS WILD-TYPE                                                229
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12P LOSS MUTATED                                            0
  12P LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  12P LOSS MUTATED                                               5
  12P LOSS WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  12P LOSS MUTATED                                1
  12P LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  12P LOSS MUTATED                                    0
  12P LOSS WILD-TYPE                                  4
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  12P LOSS MUTATED                              0                             4
  12P LOSS WILD-TYPE                            2                            15
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  12P LOSS MUTATED                                 0
  12P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  12P LOSS MUTATED                                               1
  12P LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  12P LOSS MUTATED                              1
  12P LOSS WILD-TYPE                            6
D63V9, multiclass
                                                    clus
vv                                                   12P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               65
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   12P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                229
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  4
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      15
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     3  95
  12P LOSS WILD-TYPE  18 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3   95
  12P LOSS WILD-TYPE   18  346
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 3                 18
  YES               95                346
[1] 2 2
[1] FALSE
D63V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    62   1   1   3
  12P LOSS WILD-TYPE 256  10   3  16
D63V12, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               62                256
  R1                1                 10
  R2                1                  3
  RX                3                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     1
  12P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                          10    79
  12P LOSS WILD-TYPE                        16   283
D63V13, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                      10                 16
  WHITE                                          79                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"
D63V14, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2  79
  12P LOSS WILD-TYPE   5 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   79
  12P LOSS WILD-TYPE    5  253
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               79                253
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    56  15
  12Q LOSS WILD-TYPE 265  67
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                71                332 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                 67 
$`12Q LOSS MUTATED`
TCGA-05-4426 TCGA-05-5428 TCGA-38-4632 TCGA-38-6178 TCGA-44-2657 TCGA-44-2661 
         791          670         1357          448          400          741 
TCGA-44-6775 TCGA-44-6779 TCGA-44-7662 TCGA-44-7671 TCGA-44-8120 TCGA-44-A47F 
         705         1978          218          535          260          337 
TCGA-44-A4SU TCGA-49-4501 TCGA-49-4510 TCGA-49-6743 TCGA-49-6744 TCGA-50-5049 
          76         1421          896          369          890         2146 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-6980 
        1499         1091          686         1015          701           67 
TCGA-55-7283 TCGA-55-7727 TCGA-55-7914 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 
          35           34            3          228            9          202 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A4DG 
         536           48           49           33           29          162 
TCGA-62-A46U TCGA-64-5778 TCGA-67-6217 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 
        2067         1305          422          690          165          184 
TCGA-69-8253 TCGA-71-6725 TCGA-73-4658 TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 
         100           61         1600           38          621         1970 
TCGA-78-7147 TCGA-78-7153 TCGA-78-7535 TCGA-86-8074 TCGA-86-8075 TCGA-86-8280 
        1950          760         1972           24          479           16 
TCGA-91-6829 TCGA-91-6847 TCGA-91-7771 TCGA-95-7039 TCGA-95-7043 TCGA-95-7948 
        1940          842          492           34            2          476 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-8177 TCGA-99-7458 TCGA-99-8025 
         964         1965          775          147          392          427 
TCGA-J2-A4AD TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4TC TCGA-MP-A4TK 
         287          285          353         1944         1971 

$`12Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 
        1431          578          610         1958         1997          455 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 
         912          365          913          669          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
         761          730          457          151          882           30 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          62           14          225          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 
        1971          133         1324         1429         1367         1280 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        1301           97          246         1130         1163         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
         190          722         1013          863          383          723 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
         328          302          845          704          658         1938 
TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 
        1942         1864          444          592          366          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 
        1970          882          719          385           99          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 
         466          287          351          415         1932         1081 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
         428          999          268          157         1700          445 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         522          354         2174          455          785          944 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         246          282          267         2370          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         883          764          255          105         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
         424          280         1178         1479         1375           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
           2          993           24         1239           25         1475 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 
        1826         1233         2151         1170           18          121 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
           6            4           95           40         1958           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
          39           24           54           19           16          197 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
          21           31            5           33           21          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
           6           43           26            4           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
          29           11            8           15            3          146 
TCGA-55-8615 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 
          15           66          106           42           48         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 
           1           28            5           47         1216         1289 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1970         2696         1445         2199         1246          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        1728          628         1189         1686         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        1959           62          864         1559          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         610          573          427          385          174          141 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
         202          186          414          230           70           89 
TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 
         382           77          129          214          711          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
         800          467          131           40          164          519 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
        1967         1956         1965         1973         1988         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1093         1963         1202         1948         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1963         1221          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1965         1949         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881         1952          994         1949         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
          11          630          422         1968          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
         508          745           10         1963           13          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
         476          482         1955           19           26           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          45           34           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
          10           30           14           39          323           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 
         310           79          417          372          224           35 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         197          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK 
         127          186          568          377          477          121 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932         1332          181           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
        1965           87           15          148          115          197 
TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         271          459           44          170          154          114 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         282          238          578          435          116            6 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
         622         1946         1967         1951         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1957         1980         1951         1970         1970          142 
TCGA-MP-A4TI TCGA-MP-A5C7 
        1955         1490 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                  1 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              2146               2696 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             476.0              462.5 
[1] "2.0 - 2146.0 (476.0)" "1.0 - 2696.0 (462.5)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  12Q LOSS MUTATED         0       15       30         8        15         14
  12Q LOSS WILD-TYPE       4       98      101        35        54         53
                    vv
clus                 STAGE IIIB STAGE IV
  12Q LOSS MUTATED            1        4
  12Q LOSS WILD-TYPE         10       19
D64V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                 15                 98
  STAGE IB                 30                101
  STAGE IIA                 8                 35
  STAGE IIB                15                 54
  STAGE IIIA               14                 53
  STAGE IIIB                1                 10
  STAGE IV                  4                 19
[1] 8 2
[1] 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    21  55   7   3
  12Q LOSS WILD-TYPE 122 204  33  15
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               21                122
  T2               55                204
  T3                7                 33
  T4                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                  N0  N1 N2+N3
  12Q LOSS MUTATED    51  21    14
  12Q LOSS WILD-TYPE 244  64    58
D64V5, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0                  51                244
  N1                  21                 64
  N2+N3               14                 58
[1] 3 2
[1] 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 M1B  MX
  12Q LOSS MUTATED    51   3   0   0  32
  12Q LOSS WILD-TYPE 266  15   1   3  87
D64V6, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                51                266
  M1                 3                 15
  M1A                0                  1
  M1B                0                  3
  MX                32                 87
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    58  29
  12Q LOSS WILD-TYPE 190 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     58   29
  12Q LOSS WILD-TYPE  190  185
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               58                190
  MALE                 29                185
[1] 2 2
[1] FALSE
D64V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12Q LOSS MUTATED                            1
  12Q LOSS WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12Q LOSS MUTATED                                  21
  12Q LOSS WILD-TYPE                                72
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                   51
  12Q LOSS WILD-TYPE                                                243
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12Q LOSS MUTATED                                            0
  12Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  12Q LOSS MUTATED                                               7
  12Q LOSS WILD-TYPE                                            12
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  12Q LOSS MUTATED                                1
  12Q LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  12Q LOSS MUTATED                                    0
  12Q LOSS WILD-TYPE                                  4
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  12Q LOSS MUTATED                              0                             4
  12Q LOSS WILD-TYPE                            2                            15
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  12Q LOSS MUTATED                                 0
  12Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  12Q LOSS MUTATED                                               1
  12Q LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  12Q LOSS MUTATED                              1
  12Q LOSS WILD-TYPE                            6
D64V9, multiclass
                                                    clus
vv                                                   12Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               51
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     7
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   12Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  72
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                243
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      12
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  4
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      15
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     2  85
  12Q LOSS WILD-TYPE  19 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   85
  12Q LOSS WILD-TYPE   19  356
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 2                 19
  YES               85                356
[1] 2 2
[1] FALSE
D64V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    54   1   1   3
  12Q LOSS WILD-TYPE 264  10   3  16
D64V12, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               54                264
  R1                1                 10
  R2                1                  3
  RX                3                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     1
  12Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                          10    69
  12Q LOSS WILD-TYPE                        16   293
D64V13, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                      10                 16
  WHITE                                          69                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"
D64V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  69
  12Q LOSS WILD-TYPE   6 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   69
  12Q LOSS WILD-TYPE    6  263
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               69                263
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   155  41
  13Q LOSS WILD-TYPE 166  41
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               196                207 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                41                 41 
$`13Q LOSS MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 
        1369         1126         1431          610          455          912 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 
         913          669          761          761          151          882 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 
         225          182          264         1952         1492          864 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-5643 TCGA-44-5644 TCGA-44-6147 
        1357          448         1429         1013          863          845 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
        1942         1864         1978          218          557         1970 
TCGA-44-7670 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F 
         882           99          260          486          287          337 
TCGA-44-A4SU TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
          76         1421          428          999          268          896 
TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 
         157          369          890          354         2174          455 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
        1499          282          267         2370          653          567 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 
         764          686         1015          255          105          424 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
         280         1479         1375           87          993           24 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
          25         1475           67         1233         2151         1170 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7815 TCGA-55-7903 
           6            4           40         1958           54           19 
TCGA-55-7911 TCGA-55-7994 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8207 
          21           31            6           43            4           66 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          44           23            8           15          228            9 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A491 
         202          536           15           48           29         1952 
TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U 
          28          162         1216         1289         2696         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
        2199         1246          910         1728          628         1686 
TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-6217 
        1968          864         1559          866           31          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 
         202          186          414          165           70           89 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
         129          214           61         1600          711          912 
TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
         467           40          519         1965         1973         1988 
TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7539 
        1950         1948         1957          678          215          327 
TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
        1949         1954          824           11          630          422 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8279 
         591         1963          745           10          479          482 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8673 
          16           19           26           45           34          455 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
          10           30          323         1940          310           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-8499 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 
         417          372           36          186           34          568 
TCGA-95-7948 TCGA-97-7546 TCGA-97-7554 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 
         476          964          775         1965          147          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
         115          197          392          427          459           44 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         170          154          114          287          282          238 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 
         578          116         1946         1951         1954         1980 
TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1944         1970         1955         1971 

$`13Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 
        1523          607          426         1947          578         1958 
TCGA-05-4415 TCGA-05-4422 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 
        1997          365          791          791          730          457 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 
         670           30           62           14         1962         1147 
TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 
        1073          354         1971          133         1324          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1367          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
        1130         1163         1036          190          722          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         723          328          302          704          658          705 
TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 
        1938          444          592          366          535          719 
TCGA-44-8117 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 
         385          466          351          415         1932         1081 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
        1700          445          522         2146          785          944 
TCGA-50-5072 TCGA-50-5932 TCGA-50-5942 TCGA-53-7624 TCGA-53-7626 TCGA-55-1592 
         246         1091          883         1986         1971          701 
TCGA-55-1594 TCGA-55-6543 TCGA-55-6969 TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 
        1178            2         1239         1826           18           35 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
         121           95           39           39           34           24 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          16          197            3            5           33           21 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
         100           26           47           15           33           46 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 
         216           29           11            3          146           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 
          66          106           33           42           48            1 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-64-1678 TCGA-64-1680 
           5           47         1970         1445         1189         1126 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        1959           62         1305          610          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 
         385          174          141          690          230          184 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 
         382          100           77          800          131          164 
TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 
          38          621         1970         1967         1956         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
        1093         1963         1202          760         1961         1963 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        1221         1940         1950         1934         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1972         1949         1944          881         1952          994 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 
        1971         1981         1964         1965         1972         1959 
TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
        1968          508         1963           13           24          489 
TCGA-86-8278 TCGA-86-8281 TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
         476         1955           35           18           15          405 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
          14           39           60          842          224           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         492          197          174           44          218          297 
TCGA-93-7348 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7547 
         127            2          377          477          121         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
        1932         1332          181           22          107          182 
TCGA-97-8175 TCGA-97-8179 TCGA-97-A4M7 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-MN-A4N1 
          87           15          271          435            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA 
         622          353         1967         1954         1957         1951 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 
        1970          142         1490 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 4                  1 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              2696               2146 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               457                476 
[1] "4.0 - 2696.0 (457.0)" "1.0 - 2146.0 (476.0)"
[1] "hr=" "1"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  13Q LOSS MUTATED         3       48       63        20        40         33
  13Q LOSS WILD-TYPE       1       65       68        23        29         34
                    vv
clus                 STAGE IIIB STAGE IV
  13Q LOSS MUTATED            6       10
  13Q LOSS WILD-TYPE          5       13
D65V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   3                  1
  STAGE IA                 48                 65
  STAGE IB                 63                 68
  STAGE IIA                20                 23
  STAGE IIB                40                 29
  STAGE IIIA               33                 34
  STAGE IIIB                6                  5
  STAGE IV                 10                 13
[1] 8 2
[1] 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    61 131  21   9
  13Q LOSS WILD-TYPE  82 128  19   9
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               61                 82
  T2              131                128
  T3               21                 19
  T4                9                  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
  13Q LOSS MUTATED   137  46    36
  13Q LOSS WILD-TYPE 158  39    36
D65V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                 137                158
  N1                  46                 39
  N2+N3               36                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  13Q LOSS MUTATED   147   8   0   1  65
  13Q LOSS WILD-TYPE 170  10   1   2  54
D65V6, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               147                170
  M1                 8                 10
  M1A                0                  1
  M1B                1                  2
  MX                65                 54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   121 102
  13Q LOSS WILD-TYPE 127 112
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    121  102
  13Q LOSS WILD-TYPE  127  112
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE              121                127
  MALE                102                112
[1] 2 2
[1] FALSE
D65V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  13Q LOSS MUTATED                            9
  13Q LOSS WILD-TYPE                          4
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  13Q LOSS MUTATED                                  45
  13Q LOSS WILD-TYPE                                48
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                  143
  13Q LOSS WILD-TYPE                                                151
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  13Q LOSS MUTATED                                            1
  13Q LOSS WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  13Q LOSS MUTATED                                               9
  13Q LOSS WILD-TYPE                                            10
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  13Q LOSS MUTATED                                2
  13Q LOSS WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  13Q LOSS MUTATED                                    2
  13Q LOSS WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  13Q LOSS MUTATED                              0                             8
  13Q LOSS WILD-TYPE                            2                            11
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  13Q LOSS MUTATED                                 0
  13Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  13Q LOSS MUTATED                                               2
  13Q LOSS WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  13Q LOSS MUTATED                              2
  13Q LOSS WILD-TYPE                            5
D65V9, multiclass
                                                    clus
vv                                                   13Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              143
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     9
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     8
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   13Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                151
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      10
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      11
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        5
[1] 12  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     8 215
  13Q LOSS WILD-TYPE  13 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8  215
  13Q LOSS WILD-TYPE   13  226
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 8                 13
  YES              215                226
[1] 2 2
[1] FALSE
D65V11, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED   153   7   2   9
  13Q LOSS WILD-TYPE 165   4   2  10
D65V12, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0              153                165
  R1                7                  4
  R2                2                  2
  RX                9                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     5
  13Q LOSS WILD-TYPE                                0     1
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          16   171
  13Q LOSS WILD-TYPE                        10   191
D65V13, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           5                  1
  BLACK OR AFRICAN AMERICAN                      16                 10
  WHITE                                         171                191
[1] 4 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     4 163
  13Q LOSS WILD-TYPE   3 169
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4  163
  13Q LOSS WILD-TYPE    3  169
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              163                169
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    75  19
  14Q LOSS WILD-TYPE 246  63
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                94                309 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                19                 63 
$`14Q LOSS MUTATED`
TCGA-05-4396 TCGA-05-4398 TCGA-05-4405 TCGA-05-4420 TCGA-05-4427 TCGA-05-5425 
        1947         1431          610          912          791          882 
TCGA-38-4625 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-44-2662 TCGA-44-3398 
        1952         1492          354         1357         1280         1163 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6145 TCGA-44-6146 TCGA-44-6775 TCGA-44-7669 
        1013          863          328          302          705         1970 
TCGA-44-7671 TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SS TCGA-49-4507 TCGA-49-4510 
         535          260          337          415          268          896 
TCGA-49-4514 TCGA-49-6742 TCGA-50-5068 TCGA-50-5931 TCGA-50-6597 TCGA-55-1592 
        1700          445         1499          267         1015          701 
TCGA-55-1595 TCGA-55-1596 TCGA-55-7281 TCGA-55-7283 TCGA-55-7727 TCGA-55-8092 
        1479         1375           18           35           34           26 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 TCGA-55-A491 
           4           15           29           15          202         1952 
TCGA-55-A492 TCGA-62-8398 TCGA-62-A46U TCGA-62-A471 TCGA-64-1680 TCGA-64-5778 
           1         1970         2067         1246         1126         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3774 TCGA-67-6217 TCGA-69-7761 TCGA-69-7765 
         864         1559          385          422          186          165 
TCGA-69-7980 TCGA-69-A59K TCGA-73-4662 TCGA-73-4675 TCGA-75-6214 TCGA-75-7027 
         382          214          912           40         1970         1956 
TCGA-78-7146 TCGA-78-7150 TCGA-78-7535 TCGA-78-8640 TCGA-86-7711 TCGA-86-7713 
        1988         1963         1972         1949          630          422 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8279 TCGA-86-8359 
         591         1963          745         1963          482           26 
TCGA-86-8669 TCGA-86-8672 TCGA-91-6830 TCGA-91-6848 TCGA-93-7347 TCGA-95-7039 
          34           15           60          224          297           34 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-97-7547 TCGA-97-8174 TCGA-97-8177 
         568          377          476         1965         1965          147 
TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-MN-A4N1 
         427           44          170          287          238          285 
TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TC 
        1967         1954         1957         1944 

$`14Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4403 
        1523          607          426         1369         1126          578 
TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        1958         1997          455          365          913          669 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
         791          761          761          730          457          151 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
         670           30           62           14          225          182 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 
         264         1962         1147          864         1073          448 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
        1971          133         1324         1429          400         1367 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 
         741         1301           97          246         1130         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6147 TCGA-44-6148 
         190          722          383          723          845          704 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         658         1938         1942         1864         1978          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7672 
         592          366          218          557          882          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
         385           99          486          466          287          351 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
          76         1932         1081         1421          428          999 
TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
         157          369          890          522          354         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
        2146          455          785          944          246          282 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
         686          255          105         1986         1971          424 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
         280         1178           87            2          993           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
        1239           25         1475           67         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        2151         1170          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
          40         1958           39           39           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          19           16          197           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33           21          100            6           43 
TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
          47           33           46           66          216           44 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          23           11            8          228            9            3 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         146          536           15           48           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
         106           33           42           29           48           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
           5           47          162         1216         1289         2696 
TCGA-62-8402 TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
        1445         2199          910         1728          628         1189 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 
        1686         1968         1959           62          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
         610          573          427          174          141          202 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         690          414          230          184           70           89 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         100           77          129           61         1600          711 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         800          467          131          164           38          621 
TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
         519         1967         1965         1973         1950         1944 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1093         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1963         1221          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1965         1949         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
         881         1952          994         1971         1981         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1964         1965         1972          824         1959           11 
TCGA-86-7714 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
        1968          508           10           13           24          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 
         489          476           16         1955           19           35 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          45           18          455          405           10           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
          14           39          323         1940          310           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         417          372          842           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 
         174           36           44          218          127          186 
TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 
           2          477          121          964         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
         775          181           22          107          182           87 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
          15          148          115          197          271          392 
TCGA-99-8028 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
         459          154          114          282          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 
         116            6          622          353         1946         1951 
TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1954         1980         1951         1970         1970          142 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                  2 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              2067               2696 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             600.5              455.0 
[1] "1.0 - 2067.0 (600.5)" "2.0 - 2696.0 (455.0)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  14Q LOSS MUTATED         1       18       27        10        20         19
  14Q LOSS WILD-TYPE       3       95      104        33        49         48
                    vv
clus                 STAGE IIIB STAGE IV
  14Q LOSS MUTATED            2        6
  14Q LOSS WILD-TYPE          9       17
D66V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 18                 95
  STAGE IB                 27                104
  STAGE IIA                10                 33
  STAGE IIB                20                 49
  STAGE IIIA               19                 48
  STAGE IIIB                2                  9
  STAGE IV                  6                 17
[1] 8 2
[1] 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    25  62  11   4
  14Q LOSS WILD-TYPE 118 197  29  14
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               25                118
  T2               62                197
  T3               11                 29
  T4                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                  N0  N1 N2+N3
  14Q LOSS MUTATED    57  27    18
  14Q LOSS WILD-TYPE 238  58    54
D66V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                  57                238
  N1                  27                 58
  N2+N3               18                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  14Q LOSS MUTATED    76   4   0   1  21
  14Q LOSS WILD-TYPE 241  14   1   2  98
D66V6, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                76                241
  M1                 4                 14
  M1A                0                  1
  M1B                1                  2
  MX                21                 98
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    50  53
  14Q LOSS WILD-TYPE 198 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     50   53
  14Q LOSS WILD-TYPE  198  161
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               50                198
  MALE                 53                161
[1] 2 2
[1] FALSE
D66V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  14Q LOSS MUTATED                            3
  14Q LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  14Q LOSS MUTATED                                  22
  14Q LOSS WILD-TYPE                                71
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                   66
  14Q LOSS WILD-TYPE                                                228
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  14Q LOSS MUTATED                                            0
  14Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  14Q LOSS MUTATED                                               3
  14Q LOSS WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  14Q LOSS MUTATED                                1
  14Q LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  14Q LOSS MUTATED                                    0
  14Q LOSS WILD-TYPE                                  4
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  14Q LOSS MUTATED                              1                             4
  14Q LOSS WILD-TYPE                            1                            15
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  14Q LOSS MUTATED                                 0
  14Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  14Q LOSS MUTATED                                               0
  14Q LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  14Q LOSS MUTATED                              3
  14Q LOSS WILD-TYPE                            4
D66V9, multiclass
                                                    clus
vv                                                   14Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               66
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                0
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   14Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                228
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  4
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      15
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        4
[1] 12  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  99
  14Q LOSS WILD-TYPE  17 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4   99
  14Q LOSS WILD-TYPE   17  342
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 4                 17
  YES               99                342
[1] 2 2
[1] FALSE
D66V11, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    74   0   0   5
  14Q LOSS WILD-TYPE 244  11   4  14
D66V12, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               74                244
  R1                0                 11
  R2                0                  4
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     2
  14Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          12    73
  14Q LOSS WILD-TYPE                        14   289
D66V13, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                      12                 14
  WHITE                                          73                289
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     2  79
  14Q LOSS WILD-TYPE   5 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   79
  14Q LOSS WILD-TYPE    5  253
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               79                253
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   152  35
  15Q LOSS WILD-TYPE 169  47
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               187                216 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                35                 47 
$`15Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4398 TCGA-05-4410 TCGA-05-4417 TCGA-05-4424 
        1523          607         1431         1958          455          913 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 
         761          761          882          670          225          182 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 
         264         1952         1147         1492         1073          354 
TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2668 
         448         1429          400         1367         1280          246 
TCGA-44-3918 TCGA-44-3919 TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 
        1036          190          723          845          658          705 
TCGA-44-6777 TCGA-44-6778 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
        1942         1864          592          366          218          557 
TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
         882          719          385           99          337         1421 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
         896         1700          890          354         2174         2146 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 
         455          944         2370          653          567          686 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
        1015          255          105         1971          424          280 
TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6969 
         701         1479         1375           87          993         1239 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 
          25           67         1826           18           35           95 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 
          40           34           54           19            3           31 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8205 TCGA-55-8301 TCGA-55-8507 
         100           43            4           33           44            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
          15          228            9          536           15           48 
TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
          66           33           29           48         1952           28 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 
          47          162         1289          910         1728         1686 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 
        1968         1959         1305          864           31          573 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-A59K 
         165          230          184           70           89          214 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 
         711          912          800          467           40          519 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1970         1967         1965         1973         1988         1950 
TCGA-78-7153 TCGA-78-7158 TCGA-78-7159 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
         760         1963         1221         1937         1972         1949 
TCGA-78-7542 TCGA-78-8640 TCGA-80-5608 TCGA-86-7701 TCGA-86-7954 TCGA-86-8073 
        1952         1949         1972           11         1963           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 
          24          479          482           19           26           34 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
          10           30          323         1940          310           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BC 
         417          372          842          224           36           44 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-97-7546 
         297          127          186           34          568          964 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8177 TCGA-99-7458 TCGA-99-8025 
         775          181          182          147          392          427 
TCGA-99-8028 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 
         459          154          287          238          578          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
           6          285          622         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
        1954         1957         1944         1970         1970         1955 
TCGA-MP-A4TK 
        1971 

$`15Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 
         426         1369         1126         1947          578          610 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
        1997          912          365          669          791          791 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         730          457          151           30           62           14 
TCGA-38-4626 TCGA-38-4629 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
        1962          864         1357         1971          133         1324 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 
         741         1301           97         1130         1163          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
        1013          863          383          328          302          704 
TCGA-44-6776 TCGA-44-6779 TCGA-44-7659 TCGA-44-7669 TCGA-44-7671 TCGA-44-8120 
        1938         1978          444         1970          535          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         486          466          287          351          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 
        1932         1081          428          999          268          157 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 
         445          369          522          785         1499          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5942 TCGA-50-5944 TCGA-53-7624 
         282          267         1091          883          764         1986 
TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 TCGA-55-6972 TCGA-55-6985 TCGA-55-6986 
        1178            2           24         1475         1233         2151 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        1170          121            6            4         1958           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 
          39           24           16          197           21            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
          33           21            6           26           47           15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          46           66          216           23           29           11 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48Y 
           3          146          202           49          106           42 
TCGA-55-A492 TCGA-55-A494 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
           1            5         1216         1970         2696         1445 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 
        2067         2199         1246          628         1189         1126 
TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 
          62         1559          866          610          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         174          141          422          202          186          690 
TCGA-69-7764 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 
         414          382          100           77          129           61 
TCGA-73-4658 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 
        1600          131          164           38          621         1956 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 
        1944         1093         1963         1202         1948         1957 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1961          678          215         1940         1950         1934 
TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 
        1965         1944          327          881          994         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 
        1981         1954         1964         1965          824         1959 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
         630          422         1968          591          508          745 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 
          10         1963          489          476           16         1955 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          35           45           18           15          455          405 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
          14           39           60           35          492          197 
TCGA-91-8497 TCGA-91-A4BD TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
         174          218            2          377          477          476 
TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 
         121         1965         1932         1332           22          107 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
        1965           87           15          148          115          197 
TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E6 
         271           44          170          114          282          435 
TCGA-MN-A4N5 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A5C7 
         353         1954         1980         1951          142         1490 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                  1 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              2370               2696 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             519.0              444.5 
[1] "3.0 - 2370.0 (519.0)" "1.0 - 2696.0 (444.5)"
[1] "hr=" "1.2"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  15Q LOSS MUTATED         2       51       66        22        28         33
  15Q LOSS WILD-TYPE       2       62       65        21        41         34
                    vv
clus                 STAGE IIIB STAGE IV
  15Q LOSS MUTATED            6       10
  15Q LOSS WILD-TYPE          5       13
D67V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                 51                 62
  STAGE IB                 66                 65
  STAGE IIA                22                 21
  STAGE IIB                28                 41
  STAGE IIIA               33                 34
  STAGE IIIB                6                  5
  STAGE IV                 10                 13
[1] 8 2
[1] 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    69 123  18   8
  15Q LOSS WILD-TYPE  74 136  22  10
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               69                 74
  T2              123                136
  T3               18                 22
  T4                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                  N0  N1 N2+N3
  15Q LOSS MUTATED   137  39    37
  15Q LOSS WILD-TYPE 158  46    35
D67V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                 137                158
  N1                  39                 46
  N2+N3               37                 35
[1] 3 2
[1] 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 M1B  MX
  15Q LOSS MUTATED   150   7   0   2  58
  15Q LOSS WILD-TYPE 167  11   1   1  61
D67V6, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               150                167
  M1                 7                 11
  M1A                0                  1
  M1B                2                  1
  MX                58                 61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   120  98
  15Q LOSS WILD-TYPE 128 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    120   98
  15Q LOSS WILD-TYPE  128  116
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              120                128
  MALE                 98                116
[1] 2 2
[1] FALSE
D67V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  15Q LOSS MUTATED                            5
  15Q LOSS WILD-TYPE                          8
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  15Q LOSS MUTATED                                  33
  15Q LOSS WILD-TYPE                                60
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                  155
  15Q LOSS WILD-TYPE                                                139
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  15Q LOSS MUTATED                                            0
  15Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  15Q LOSS MUTATED                                               9
  15Q LOSS WILD-TYPE                                            10
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  15Q LOSS MUTATED                                1
  15Q LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  15Q LOSS MUTATED                                    3
  15Q LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  15Q LOSS MUTATED                              0                             8
  15Q LOSS WILD-TYPE                            2                            11
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  15Q LOSS MUTATED                                 1
  15Q LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  15Q LOSS MUTATED                                               1
  15Q LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  15Q LOSS MUTATED                              2
  15Q LOSS WILD-TYPE                            5
D67V9, multiclass
                                                    clus
vv                                                   15Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              155
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     9
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     8
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   15Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                139
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      10
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      11
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        5
[1] 12  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    11 207
  15Q LOSS WILD-TYPE  10 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     11  207
  15Q LOSS WILD-TYPE   10  234
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                11                 10
  YES              207                234
[1] 2 2
[1] FALSE
D67V11, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED   150   6   2  10
  15Q LOSS WILD-TYPE 168   5   2   9
D67V12, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0              150                168
  R1                6                  5
  R2                2                  2
  RX               10                  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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  1     4
  15Q LOSS WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                          12   171
  15Q LOSS WILD-TYPE                        14   191
D67V13, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  2
  BLACK OR AFRICAN AMERICAN                      12                 14
  WHITE                                         171                191
[1] 4 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     3 157
  15Q LOSS WILD-TYPE   4 175
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3  157
  15Q LOSS WILD-TYPE    4  175
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              157                175
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    67  17
  16P LOSS WILD-TYPE 254  65
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                84                319 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                17                 65 
$`16P LOSS MUTATED`
TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 
        1369         1947         1431         1997          912          913 
TCGA-05-4427 TCGA-35-4122 TCGA-44-3918 TCGA-44-5643 TCGA-44-6777 TCGA-44-7660 
         791          225         1036         1013         1942          592 
TCGA-44-7661 TCGA-44-8117 TCGA-44-8119 TCGA-49-4494 TCGA-49-4510 TCGA-49-6742 
         366          385           99         1081          896          445 
TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5066 TCGA-50-5068 TCGA-50-5946 
         369          522          354          944         1499          686 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6971 TCGA-55-6986 
        1986          424          280           87           25         2151 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 TCGA-55-7914 TCGA-55-8094 TCGA-55-8205 
          40           34           19            3            4           33 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8616 TCGA-55-A491 TCGA-62-8397 
          29           11            8           48         1952         1289 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
        1445         2067         2199         1246          910          628 
TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-69-7763 TCGA-69-7974 TCGA-69-8255 
         864           31          610          690          184          129 
TCGA-69-A59K TCGA-73-4662 TCGA-75-6214 TCGA-78-7146 TCGA-78-7149 TCGA-78-7167 
         214          912         1970         1988         1093         1937 
TCGA-78-7535 TCGA-78-7536 TCGA-83-5908 TCGA-86-6851 TCGA-86-7953 TCGA-86-8054 
        1972         1949          824         1959          591          745 
TCGA-86-8073 TCGA-86-8672 TCGA-91-6829 TCGA-91-6831 TCGA-91-6847 TCGA-91-7771 
          13           15         1940          310          842          492 
TCGA-91-8499 TCGA-95-7567 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-L4-A4E5 
          36          568          775          181          107          578 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TF TCGA-MP-A4TI 
         116            6          285         1957         1970         1955 

$`16P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4403 TCGA-05-4405 
        1523          607          426         1126          578          610 
TCGA-05-4410 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
        1958          455          365          669          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          730          457          151          882          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          30           62           14          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        1962         1147         1492          864         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1357          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
         246         1130         1163          190          722          863 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
         383          723          328          302          845          704 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
         658          705         1938         1864         1978          444 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
         218          557         1970          882          535          719 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
         260          486          466          287          337          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
         415           76         1932         1421          428          999 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-50-5045 TCGA-50-5049 
         268          157         1700          890         2174         2146 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         455          785          246          282          267         1091 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 
        2370          653          567          883          764         1015 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
         255          105         1971          701         1178         1479 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 
        1375            2          993           24         1239         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
          67         1826         1233         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
         121            6            4           95         1958           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          39           24           54           16          197           21 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33           21          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 
          43           26           47           15           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
         216           44           23           15          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 
           3          146          202          536           15           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          66          106           33           42           29           48 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
           1           28            5           47          162         1216 
TCGA-62-8398 TCGA-62-8399 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
        1970         2696         1728         1189         1686         1126 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 
        1968         1959           62         1305         1559          866 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         573          427          385          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 
         202          186          414          165          230           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 
          89          382          100           77           61         1600 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         711          800          467          131           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
          38          621          519         1967         1956         1965 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1973         1950         1944         1963         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
        1948         1957         1961         1963         1221          678 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 
         215         1940         1950         1934         1965         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
         327          881         1952          994         1949         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-7701 
        1981         1954         1964         1965         1972           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
         630          422         1968         1963          508           10 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        1963           24          479          489          476          482 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
          16         1955           19           26           35           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          34           18          455          405           10           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
          14           39          323           60           79          417 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
         372          224           35          197          174           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         218          297          127          186           34            2 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 
         377          477          476          121          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        1932         1332           22          182         1965           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
         147           15          148          115          197          271 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         392          427          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MN-A4N4 
         114          287          282          238          435          622 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
         353         1946         1967         1951         1954         1954 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK 
        1980         1951         1944         1970          142         1971 
TCGA-MP-A5C7 
        1490 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                  1 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              2199               2696 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               657                435 
[1] "3.0 - 2199.0 (657.0)" "1.0 - 2696.0 (435.0)"
[1] "hr=" "1.4"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  16P LOSS MUTATED         1       19       22         7        19         20
  16P LOSS WILD-TYPE       3       94      109        36        50         47
                    vv
clus                 STAGE IIIB STAGE IV
  16P LOSS MUTATED            6        7
  16P LOSS WILD-TYPE          5       16
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 19                 94
  STAGE IB                 22                109
  STAGE IIA                 7                 36
  STAGE IIB                19                 50
  STAGE IIIA               20                 47
  STAGE IIIB                6                  5
  STAGE IV                  7                 16
[1] 8 2
[1] 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    28  56  11   6
  16P LOSS WILD-TYPE 115 203  29  12
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               28                115
  T2               56                203
  T3               11                 29
  T4                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                  N0  N1 N2+N3
  16P LOSS MUTATED    59  16    24
  16P LOSS WILD-TYPE 236  69    48
D68V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                  59                236
  N1                  16                 69
  N2+N3               24                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  16P LOSS MUTATED    66   5   1   1  28
  16P LOSS WILD-TYPE 251  13   0   2  91
D68V6, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                66                251
  M1                 5                 13
  M1A                1                  0
  M1B                1                  2
  MX                28                 91
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    51  50
  16P LOSS WILD-TYPE 197 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     51   50
  16P LOSS WILD-TYPE  197  164
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               51                197
  MALE                 50                164
[1] 2 2
[1] FALSE
D68V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16P LOSS MUTATED                            4
  16P LOSS WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16P LOSS MUTATED                                  24
  16P LOSS WILD-TYPE                                69
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                   60
  16P LOSS WILD-TYPE                                                234
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16P LOSS MUTATED                                            0
  16P LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  16P LOSS MUTATED                                               5
  16P LOSS WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  16P LOSS MUTATED                                1
  16P LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  16P LOSS MUTATED                                    1
  16P LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  16P LOSS MUTATED                              0                             3
  16P LOSS WILD-TYPE                            2                            16
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  16P LOSS MUTATED                                 0
  16P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  16P LOSS MUTATED                                               1
  16P LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  16P LOSS MUTATED                              2
  16P LOSS WILD-TYPE                            5
D68V9, multiclass
                                                    clus
vv                                                   16P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               60
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   16P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                234
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      16
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        5
[1] 12  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     5  96
  16P LOSS WILD-TYPE  16 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5   96
  16P LOSS WILD-TYPE   16  345
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 5                 16
  YES               96                345
[1] 2 2
[1] FALSE
D68V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    68   1   1   2
  16P LOSS WILD-TYPE 250  10   3  17
D68V12, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               68                250
  R1                1                 10
  R2                1                  3
  RX                2                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     1
  16P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           7    79
  16P LOSS WILD-TYPE                        19   283
D68V13, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       7                 19
  WHITE                                          79                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"
D68V14, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  70
  16P LOSS WILD-TYPE   4 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   70
  16P LOSS WILD-TYPE    4  262
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               70                262
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    91  20
  16Q LOSS WILD-TYPE 230  62
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               111                292 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                20                 62 
$`16Q LOSS MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4415 TCGA-05-4420 
        1369         1126         1431          610         1997          912 
TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 
         913          791          761          670          225          182 
TCGA-38-4625 TCGA-38-4628 TCGA-44-2661 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
        1952         1492          741         1036          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6777 TCGA-44-7660 TCGA-44-7661 TCGA-44-7669 
        1013          863         1942          592          366         1970 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A47B TCGA-49-4494 TCGA-49-4510 TCGA-49-6742 
         385           99          287         1081          896          445 
TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 
         369          522          354         2146          944         1499 
TCGA-50-5946 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 
         686         1986          424          280         1479           87 
TCGA-55-6971 TCGA-55-6986 TCGA-55-7281 TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 
          25         2151           18           40           34           19 
TCGA-55-8205 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8616 TCGA-55-8620 
          33           29           11            8           48           66 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-62-8397 TCGA-62-A46U TCGA-62-A472 
          29         1952           28         1289         2067          910 
TCGA-64-1677 TCGA-64-5774 TCGA-64-5778 TCGA-67-3770 TCGA-67-3771 TCGA-69-7763 
         628         1959         1305           31          610          690 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 
         184           70           89          129          214         1600 
TCGA-73-4662 TCGA-75-6214 TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
         912         1970         1988         1093         1963         1202 
TCGA-78-7159 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-83-5908 TCGA-86-6851 
        1221         1937         1972         1949          824         1959 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8073 TCGA-86-8075 
         630          422          591          745           13          479 
TCGA-86-8359 TCGA-86-8672 TCGA-91-6829 TCGA-91-6831 TCGA-91-6847 TCGA-91-7771 
          26           15         1940          310          842          492 
TCGA-91-8499 TCGA-93-7348 TCGA-95-7567 TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 
          36          127          568          964          775          181 
TCGA-97-8171 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         107          238          578          116            6          285 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TI 
        1957         1944         1955 

$`16Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 
        1523          607          426         1947          578         1958 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 
         455          365          669          791          761          730 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
         457          151          882           30           62           14 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
         264         1962         1147          864         1073          354 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
        1357          448         1971          133         1324         1429 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
         400         1367         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1130         1163          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 
         845          704          658          705         1938         1864 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 
        1978          444          218          557          882          535 
TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G 
         719          260          486          466          337          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
         415           76         1932         1421          428          999 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-50-5045 TCGA-50-5051 
         268          157         1700          890         2174          455 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
         785          246          282          267         1091         2370 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 
         653          567          883          764         1015          255 
TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 
         105         1971          701         1178         1375            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
         993           24         1239         1475           67         1826 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1233         1170           35          121            6            4 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
          95         1958           39           39           24           54 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          16          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33           21          100            6           43           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
           4           47           15           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          44           23           15          228            9            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 
         146          202          536           15           49          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF 
          33           42           48            1            5           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V 
         162         1216         1970         2696         1445         2199 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        1246         1728         1189         1686         1126         1968 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
          62          864         1559          866          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         414          165          230          382          100           77 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
          61          711          800          467          131           40 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7027 
         164           38          621          519         1967         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 
        1965         1973         1950         1944          760         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1957         1961         1963          678          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1950         1934         1965         1944          327          881 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
        1952          994         1949         1971         1981         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 
        1964         1965         1972           11         1968         1963 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
         508           10         1963           24          489          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
         482           16         1955           19           35           45 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          34           18          455          405           10           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
          14           39          323           60           79          417 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
         372          224           35          197          174           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 
         218          297          186           34            2          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         477          476          121         1965         1932         1332 
TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
          22          182         1965           87          147           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
         148          115          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         459           44          170          154          114          287 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         282          435          622          353         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE 
        1951         1954         1954         1980         1951         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1971         1490 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                  1 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              2151               2696 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               630                427 
[1] "6.0 - 2151.0 (630.0)" "1.0 - 2696.0 (427.0)"
[1] "hr=" "1.4"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  16Q LOSS MUTATED         1       29       34         9        22         20
  16Q LOSS WILD-TYPE       3       84       97        34        47         47
                    vv
clus                 STAGE IIIB STAGE IV
  16Q LOSS MUTATED            6        7
  16Q LOSS WILD-TYPE          5       16
D69V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 29                 84
  STAGE IB                 34                 97
  STAGE IIA                 9                 34
  STAGE IIB                22                 47
  STAGE IIIA               20                 47
  STAGE IIIB                6                  5
  STAGE IV                  7                 16
[1] 8 2
[1] 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    41  71  11   5
  16Q LOSS WILD-TYPE 102 188  29  13
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               41                102
  T2               71                188
  T3               11                 29
  T4                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                  N0  N1 N2+N3
  16Q LOSS MUTATED    78  22    25
  16Q LOSS WILD-TYPE 217  63    47
D69V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                  78                217
  N1                  22                 63
  N2+N3               25                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  16Q LOSS MUTATED    88   5   1   1  32
  16Q LOSS WILD-TYPE 229  13   0   2  87
D69V6, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                88                229
  M1                 5                 13
  M1A                1                  0
  M1B                1                  2
  MX                32                 87
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    65  63
  16Q LOSS WILD-TYPE 183 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     65   63
  16Q LOSS WILD-TYPE  183  151
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               65                183
  MALE                 63                151
[1] 2 2
[1] FALSE
D69V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16Q LOSS MUTATED                            5
  16Q LOSS WILD-TYPE                          8
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16Q LOSS MUTATED                                  29
  16Q LOSS WILD-TYPE                                64
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                   79
  16Q LOSS WILD-TYPE                                                215
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16Q LOSS MUTATED                                            0
  16Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  16Q LOSS MUTATED                                               6
  16Q LOSS WILD-TYPE                                            13
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  16Q LOSS MUTATED                                2
  16Q LOSS WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  16Q LOSS MUTATED                                    1
  16Q LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  16Q LOSS MUTATED                              0                             3
  16Q LOSS WILD-TYPE                            2                            16
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  16Q LOSS MUTATED                                 0
  16Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  16Q LOSS MUTATED                                               1
  16Q LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  16Q LOSS MUTATED                              2
  16Q LOSS WILD-TYPE                            5
D69V9, multiclass
                                                    clus
vv                                                   16Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                29
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               79
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     6
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   16Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  64
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                215
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      16
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        5
[1] 12  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     5 123
  16Q LOSS WILD-TYPE  16 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5  123
  16Q LOSS WILD-TYPE   16  318
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 5                 16
  YES              123                318
[1] 2 2
[1] FALSE
D69V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    89   1   1   2
  16Q LOSS WILD-TYPE 229  10   3  17
D69V12, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               89                229
  R1                1                 10
  R2                1                  3
  RX                2                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     2
  16Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           8   100
  16Q LOSS WILD-TYPE                        18   262
D69V13, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       8                 18
  WHITE                                         100                262
[1] 4 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     4  89
  16Q LOSS WILD-TYPE   3 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4   89
  16Q LOSS WILD-TYPE    3  243
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO               89                243
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   136  28
  17P LOSS WILD-TYPE 185  54
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               164                239 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                28                 54 
$`17P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4396 TCGA-05-4410 TCGA-05-4420 TCGA-05-4425 
        1523         1369         1947         1958          912          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5428 
         791          791          761          730          457          670 
TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4631 TCGA-38-4632 
          30          225          182         1952          354         1357 
TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 
         448         1429          400         1367         1280         1301 
TCGA-44-3919 TCGA-44-5643 TCGA-44-6144 TCGA-44-6775 TCGA-44-6779 TCGA-44-7660 
         190         1013          723          705         1978          592 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         366          218          882          385           99          260 
TCGA-44-A47B TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 
         287          428          268          896          157          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5051 TCGA-50-5068 TCGA-50-5931 
         890          522          354          455         1499          267 
TCGA-50-5941 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 
         567          764         1015          255         1986         1971 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 TCGA-55-6972 
         424          701         1178         1375           24         1475 
TCGA-55-6985 TCGA-55-7281 TCGA-55-7573 TCGA-55-7576 TCGA-55-7726 TCGA-55-7727 
        1233           18            4           40           39           34 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 
          19          197           21            3           31          100 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 TCGA-55-8205 TCGA-55-8510 TCGA-55-8511 
          43           26           15           33          228            9 
TCGA-55-8514 TCGA-55-8614 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 
         202          536           33           42           29         1952 
TCGA-62-8397 TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
        1289         2067          910         1728         1686         1968 
TCGA-64-5774 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-6215 
        1959          866           31          610          427          174 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
         422          202          186          414          165          184 
TCGA-69-7978 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-7499 
          70          129          214         1600          711          519 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7150 
        1970         1967         1965         1973         1988         1963 
TCGA-78-7159 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1221         1972         1949          327          881         1952 
TCGA-78-8640 TCGA-78-8655 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 
        1949         1981         1972           11          630          591 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 
        1963          745         1963           13          479          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-91-6831 TCGA-91-6840 
         482           16           19           45          310          372 
TCGA-91-6847 TCGA-91-7771 TCGA-93-7347 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
         842          492          297           34          568          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 
         477          476          121          775          181           87 
TCGA-97-8547 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD 
         148          392          427          170          154          287 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TE 
         282          578          622         1954         1957         1970 
TCGA-MP-A4TF TCGA-MP-A5C7 
        1970         1490 

$`17P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
         607          426         1126         1431          578          610 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4432 TCGA-05-5423 
        1997          455          365          913          761          151 
TCGA-05-5425 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
         882           62           14          264         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
        1492          864         1073         1971          133         1324 
TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
         741           97          246         1130         1163         1036 
TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         722          863          383          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
         704          658         1938         1942         1864          444 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A 
         557         1970          535          719          486          466 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         337          351          415           76         1932         1081 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4514 TCGA-49-6742 TCGA-50-5045 TCGA-50-5049 
        1421          999         1700          445         2174         2146 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
         785          944          246          282         1091         2370 
TCGA-50-5935 TCGA-50-5942 TCGA-50-5946 TCGA-50-8460 TCGA-53-A4EZ TCGA-55-1595 
         653          883          686          105          280         1479 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 
          87            2          993         1239           25           67 
TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        1826         2151         1170           35          121            6 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
          95         1958           39           24           54           16 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8094 TCGA-55-8096 
           5           33           21            6            4           47 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          46           66          216           44           23           29 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
          11            8           15            3          146           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A490 TCGA-55-A492 
          48           49           66          106           48            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 
          28            5           47          162         1216         1970 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 
        2696         1445         2199         1246          628         1189 
TCGA-64-1680 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3772 
        1126           62         1305          864         1559          573 
TCGA-67-3774 TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 
         385          141          690          230           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
         100           77           61          912          800          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 
         131           40          164           38          621         1956 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1950         1944         1093         1202          760         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1957         1961         1963          678          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7633 
        1950         1934         1937         1965         1944          994 
TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 
        1971         1954         1964         1965          824         1959 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8076 
         422         1968          508           10           24          489 
TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
        1955           26           35           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
         455          405           10           30           14           39 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6848 
         323         1940           60           79          417          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
          35          197          174           36           44          218 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         127          186            2          964         1965         1932 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 
        1332           22          107          182         1965          147 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 
          15          115          197          271          459           44 
TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         114          238          435          116            6          285 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T9 
         353         1946         1967         1951         1954         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1944          142         1955         1971 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                  1 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              2067               2696 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             480.5              445.0 
[1] "3.0 - 2067.0 (480.5)" "1.0 - 2696.0 (445.0)"
[1] "hr=" "1.3"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  17P LOSS MUTATED         2       36       56        20        33         33
  17P LOSS WILD-TYPE       2       77       75        23        36         34
                    vv
clus                 STAGE IIIB STAGE IV
  17P LOSS MUTATED            4       10
  17P LOSS WILD-TYPE          7       13
D70V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                 36                 77
  STAGE IB                 56                 75
  STAGE IIA                20                 23
  STAGE IIB                33                 36
  STAGE IIIA               33                 34
  STAGE IIIB                4                  7
  STAGE IV                 10                 13
[1] 8 2
[1] 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    52 118  16   7
  17P LOSS WILD-TYPE  91 141  24  11
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               52                 91
  T2              118                141
  T3               16                 24
  T4                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                  N0  N1 N2+N3
  17P LOSS MUTATED   120  38    32
  17P LOSS WILD-TYPE 175  47    40
D70V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                 120                175
  N1                  38                 47
  N2+N3               32                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  17P LOSS MUTATED   136   9   0   0  48
  17P LOSS WILD-TYPE 181   9   1   3  71
D70V6, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               136                181
  M1                 9                  9
  M1A                0                  1
  M1B                0                  3
  MX                48                 71
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   112  82
  17P LOSS WILD-TYPE 136 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    112   82
  17P LOSS WILD-TYPE  136  132
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              112                136
  MALE                 82                132
[1] 2 2
[1] FALSE
D70V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17P LOSS MUTATED                            4
  17P LOSS WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17P LOSS MUTATED                                  37
  17P LOSS WILD-TYPE                                56
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                  134
  17P LOSS WILD-TYPE                                                160
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17P LOSS MUTATED                                            2
  17P LOSS WILD-TYPE                                          2
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  17P LOSS MUTATED                                               7
  17P LOSS WILD-TYPE                                            12
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  17P LOSS MUTATED                                1
  17P LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  17P LOSS MUTATED                                    3
  17P LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  17P LOSS MUTATED                              0                             3
  17P LOSS WILD-TYPE                            2                            16
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  17P LOSS MUTATED                                 0
  17P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  17P LOSS MUTATED                                               2
  17P LOSS WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  17P LOSS MUTATED                              1
  17P LOSS WILD-TYPE                            6
D70V9, multiclass
                                                    clus
vv                                                   17P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              134
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     7
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     3
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   17P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                160
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      12
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      16
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     4 190
  17P LOSS WILD-TYPE  17 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  190
  17P LOSS WILD-TYPE   17  251
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 4                 17
  YES              190                251
[1] 2 2
[1] FALSE
D70V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   137   4   1   8
  17P LOSS WILD-TYPE 181   7   3  11
D70V12, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              137                181
  R1                4                  7
  R2                1                  3
  RX                8                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     1
  17P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                          12   151
  17P LOSS WILD-TYPE                        14   211
D70V13, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                      12                 14
  WHITE                                         151                211
[1] 4 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     5 135
  17P LOSS WILD-TYPE   2 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5  135
  17P LOSS WILD-TYPE    2  197
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  2
  NOT HISPANIC OR LATINO              135                197
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    33  11
  17Q LOSS WILD-TYPE 288  71
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                44                359 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                11                 71 
$`17Q LOSS MUTATED`
TCGA-05-4396 TCGA-35-4122 TCGA-38-4631 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 
        1947          225          354          448         1429          400 
TCGA-44-2662 TCGA-44-2665 TCGA-44-7660 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 
        1280         1301          592          428          268          157 
TCGA-49-6761 TCGA-50-5051 TCGA-50-5068 TCGA-53-7624 TCGA-55-1596 TCGA-55-6712 
         354          455         1499         1986         1375           24 
TCGA-55-7576 TCGA-55-8091 TCGA-55-8092 TCGA-55-8511 TCGA-55-8614 TCGA-62-8397 
          40           43           26            9          536         1289 
TCGA-64-1676 TCGA-67-6217 TCGA-69-7764 TCGA-69-A59K TCGA-75-7025 TCGA-75-7031 
        1728          422          414          214         1967         1965 
TCGA-78-7146 TCGA-78-7535 TCGA-78-7536 TCGA-78-8655 TCGA-86-7701 TCGA-86-8280 
        1988         1972         1949         1981           11           16 
TCGA-91-6840 TCGA-91-7771 TCGA-95-7948 TCGA-95-A4VK TCGA-J2-8192 TCGA-J2-A4AD 
         372          492          476          121          154          287 
TCGA-L4-A4E5 TCGA-MP-A5C7 
         578         1490 

$`17Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
        1523          607          426         1369         1126         1431 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
         578          610         1958         1997          455          912 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
         365          913          669          791          791          761 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
         761          730          457          151          882          670 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
          30           62           14          182          264         1952 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
        1962         1147         1492          864         1073         1357 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 
        1971          133         1324         1367          741           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1013          863          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
        1864         1978          444          366          218          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
        1970          882          535          719          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
         260          486          466          287          337          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 
         415           76         1932         1081         1421          999 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         896         1700          445          369          890          522 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
        2174         2146          785          944          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         267         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 
         764          686         1015          255          105         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 
         424          280          701         1178         1479           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
           2          993         1239           25         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
        1826         1233         2151         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
         121            6            4           95         1958           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
          39           34           24           54           19           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
         197           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
          21          100            6            4           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           46           66          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
          29           11            8           15          228            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         146          202           15           48           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
         106           33           42           29           48         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
           1           28            5           47          162         1216 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1970         2696         1445         2067         2199         1246 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
         910          628         1189         1686         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1959           62         1305          864         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
          31          610          573          427          385          174 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 
         141          202          186          690          165          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         184           70           89          382          100           77 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
         129           61         1600          711          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         467          131           40          164           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
         519         1970         1956         1973         1950         1944 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1093         1963         1202          760         1948         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
        1961         1963         1221          678          215         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 
        1950         1934         1937         1965         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 
         881         1952          994         1949         1971         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 
        1964         1965         1972          824         1959          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         422         1968          591         1963          508          745 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
          10         1963           13           24          479          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
         476          482         1955           19           26           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          45           34           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
          10           30           14           39          323         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
          60          310           79          417          842          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
          35          197          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
         297          127          186           34            2          568 
TCGA-95-7944 TCGA-95-7947 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         377          477          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
         775          181           22          107          182         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 
          87          147           15          148          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         271          392          427          459           44          170 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         114          282          238          435          116            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         285          622          353         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1954         1954         1957         1980         1951         1944 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1970         1970          142         1955         1971 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                  1 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              1988               2696 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             451.5              467.0 
[1] "9.0 - 1988.0 (451.5)" "1.0 - 2696.0 (467.0)"
[1] "hr=" "1"  
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  17Q LOSS MUTATED         1        7       14         5        10         11
  17Q LOSS WILD-TYPE       3      106      117        38        59         56
                    vv
clus                 STAGE IIIB STAGE IV
  17Q LOSS MUTATED            2        2
  17Q LOSS WILD-TYPE          9       21
D71V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                  7                106
  STAGE IB                 14                117
  STAGE IIA                 5                 38
  STAGE IIB                10                 59
  STAGE IIIA               11                 56
  STAGE IIIB                2                  9
  STAGE IV                  2                 21
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED    10  34   6   2
  17Q LOSS WILD-TYPE 133 225  34  16
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               10                133
  T2               34                225
  T3                6                 34
  T4                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                  N0  N1 N2+N3
  17Q LOSS MUTATED    29  11    11
  17Q LOSS WILD-TYPE 266  74    61
D71V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                  29                266
  N1                  11                 74
  N2+N3               11                 61
[1] 3 2
[1] 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 M1B  MX
  17Q LOSS MUTATED    35   2   0   0  14
  17Q LOSS WILD-TYPE 282  16   1   3 105
D71V6, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                35                282
  M1                 2                 16
  M1A                0                  1
  M1B                0                  3
  MX                14                105
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    29  23
  17Q LOSS WILD-TYPE 219 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     29   23
  17Q LOSS WILD-TYPE  219  191
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               29                219
  MALE                 23                191
[1] 2 2
[1] FALSE
D71V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17Q LOSS MUTATED                            0
  17Q LOSS WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17Q LOSS MUTATED                                  10
  17Q LOSS WILD-TYPE                                83
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                   39
  17Q LOSS WILD-TYPE                                                255
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17Q LOSS MUTATED                                            0
  17Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  17Q LOSS MUTATED                                               1
  17Q LOSS WILD-TYPE                                            18
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  17Q LOSS MUTATED                                0
  17Q LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  17Q LOSS MUTATED                                    1
  17Q LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  17Q LOSS MUTATED                              0                             0
  17Q LOSS WILD-TYPE                            2                            19
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  17Q LOSS MUTATED                                 0
  17Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  17Q LOSS MUTATED                                               0
  17Q LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  17Q LOSS MUTATED                              1
  17Q LOSS WILD-TYPE                            6
D71V9, multiclass
                                                    clus
vv                                                   17Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               39
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     1
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     0
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   17Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                255
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      18
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      19
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     2  50
  17Q LOSS WILD-TYPE  19 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   50
  17Q LOSS WILD-TYPE   19  391
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 2                 19
  YES               50                391
[1] 2 2
[1] FALSE
D71V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    38   2   0   2
  17Q LOSS WILD-TYPE 280   9   4  17
D71V12, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               38                280
  R1                2                  9
  R2                0                  4
  RX                2                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     1
  17Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           2    42
  17Q LOSS WILD-TYPE                        24   320
D71V13, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       2                 24
  WHITE                                          42                320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  40
  17Q LOSS WILD-TYPE   6 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   40
  17Q LOSS WILD-TYPE    6  292
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               40                292
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   106  28
  18P LOSS WILD-TYPE 215  54
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               134                269 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                28                 54 
$`18P LOSS MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4398 TCGA-05-4405 TCGA-05-4417 TCGA-05-4425 
        1523         1126         1431          610          455          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-5425 TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 
         791          791          882           62          182          264 
TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-44-2656 
        1952         1147         1492          354         1357         1429 
TCGA-44-2665 TCGA-44-3918 TCGA-44-6145 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
        1301         1036          328          705         1942         1864 
TCGA-44-6779 TCGA-44-7667 TCGA-44-7669 TCGA-44-A479 TCGA-44-A47F TCGA-44-A4SU 
        1978          557         1970          486          337           76 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 
        1421          428          999          157          445          369 
TCGA-50-5072 TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 
         246         2370          567          686         1015         1986 
TCGA-53-7626 TCGA-55-1594 TCGA-55-1596 TCGA-55-6971 TCGA-55-6972 TCGA-55-6985 
        1971         1178         1375           25         1475         1233 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7726 
          18           35            4           95           40           39 
TCGA-55-7728 TCGA-55-7910 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 
          24          197           21            6           43           15 
TCGA-55-8207 TCGA-55-8507 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
          66            8           48           66           29           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-62-8397 TCGA-62-A471 TCGA-62-A472 
        1952            1           28         1289         1246          910 
TCGA-64-1679 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1686         1559          866           31          610          573 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7765 TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 
         141          422          165           89          214           61 
TCGA-73-4666 TCGA-73-4670 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
         800          131          519         1970         1967         1956 
TCGA-75-7031 TCGA-78-7146 TCGA-78-7150 TCGA-78-7161 TCGA-78-7167 TCGA-78-7535 
        1965         1988         1963          215         1937         1972 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 
        1954          824         1959           11         1968         1963 
TCGA-86-8073 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8672 
          13          476          482           16           19           15 
TCGA-91-6830 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-A4BD 
          60          417          842          224          492          218 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-97-7547 TCGA-97-7552 
         127           34          568          476         1965         1932 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8547 TCGA-J2-8192 TCGA-J2-8194 
         181           22         1965          148          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 
         287          282          578         1967         1951         1954 
TCGA-MP-A4TF TCGA-MP-A4TI 
        1970         1955 

$`18P LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4403 TCGA-05-4410 
         607          426         1369         1947          578         1958 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 
        1997          912          365          913          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 
         730          457          151          670           30           14 
TCGA-35-4122 TCGA-38-4626 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
         225         1962          864         1073          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
         133         1324          400         1367          741         1280 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
          97          246         1130         1163          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 TCGA-44-6147 
        1013          863          383          723          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
         704          658         1938          444          592          366 
TCGA-44-7662 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
         218          882          535          719          385           99 
TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
         260          466          287          351          415         1932 
TCGA-49-4494 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 
        1081          268          896         1700          890          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         354         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 
        1499          282          267         1091          653          883 
TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         764          255          105          424          280          701 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
        1479           87            2          993           24         1239 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 
          67         1826         2151         1170          121            6 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        1958           39           34           54           19           16 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 
          21            3           31            5           33          100 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8299 
          26            4           47           33           46          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
          44           23           29           11           15          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
           9            3          146          202          536           15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A494 TCGA-55-A4DF 
          49          106           33           42            5           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U 
         162         1216         1970         2696         1445         2067 
TCGA-62-A46V TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 
        2199         1728          628         1189         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-67-3773 TCGA-67-3774 
        1959           62         1305          864          427          385 
TCGA-67-6215 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
         174          202          186          690          414          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
         184           70          382          100           77          129 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
        1600          711          912          467           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
          38          621         1973         1950         1944         1093 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1202          760         1948         1957         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
        1221          678         1940         1950         1934         1965 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1949         1944          327          881         1952          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 
        1949         1971         1981         1964         1965         1972 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
         630          422          591          508          745           10 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8281 TCGA-86-8359 
        1963           24          479          489         1955           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
          35           45           34           18          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
          10           30           14           39          323         1940 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
         310           79          372           35          197          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-93-7347 TCGA-93-8067 TCGA-95-7043 TCGA-95-7944 
          36           44          297          186            2          377 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 
         477          121          964         1332          775          107 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 
         182           87          147           15          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
         271          392          427          459           44          170 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 
         238          435          116            6          285          622 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
         353         1946         1954         1957         1980         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
        1944         1970          142         1971         1490 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  2 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              2370               2696 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               538                444 
[1] "1.0 - 2370.0 (538.0)" "2.0 - 2696.0 (444.0)"
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  18P LOSS MUTATED         1       25       47        16        30         19
  18P LOSS WILD-TYPE       3       88       84        27        39         48
                    vv
clus                 STAGE IIIB STAGE IV
  18P LOSS MUTATED            5       13
  18P LOSS WILD-TYPE          6       10
D72V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 25                 88
  STAGE IB                 47                 84
  STAGE IIA                16                 27
  STAGE IIB                30                 39
  STAGE IIIA               19                 48
  STAGE IIIB                5                  6
  STAGE IV                 13                 10
[1] 8 2
[1] 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    40  96  14   6
  18P LOSS WILD-TYPE 103 163  26  12
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               40                103
  T2               96                163
  T3               14                 26
  T4                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                  N0  N1 N2+N3
  18P LOSS MUTATED    96  35    23
  18P LOSS WILD-TYPE 199  50    49
D72V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                  96                199
  N1                  35                 50
  N2+N3               23                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  18P LOSS MUTATED    96  11   0   1  48
  18P LOSS WILD-TYPE 221   7   1   2  71
D72V6, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                96                221
  M1                11                  7
  M1A                0                  1
  M1B                1                  2
  MX                48                 71
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    98  58
  18P LOSS WILD-TYPE 150 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     98   58
  18P LOSS WILD-TYPE  150  156
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               98                150
  MALE                 58                156
[1] 2 2
[1] FALSE
D72V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18P LOSS MUTATED                            4
  18P LOSS WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18P LOSS MUTATED                                  31
  18P LOSS WILD-TYPE                                62
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                  102
  18P LOSS WILD-TYPE                                                192
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18P LOSS MUTATED                                            1
  18P LOSS WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  18P LOSS MUTATED                                               4
  18P LOSS WILD-TYPE                                            15
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  18P LOSS MUTATED                                1
  18P LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  18P LOSS MUTATED                                    3
  18P LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  18P LOSS MUTATED                              0                             6
  18P LOSS WILD-TYPE                            2                            13
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  18P LOSS MUTATED                                 1
  18P LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  18P LOSS MUTATED                                               0
  18P LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  18P LOSS MUTATED                              3
  18P LOSS WILD-TYPE                            4
D72V9, multiclass
                                                    clus
vv                                                   18P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              102
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     4
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     6
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   18P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                192
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      15
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      13
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        4
[1] 12  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     5 151
  18P LOSS WILD-TYPE  16 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5  151
  18P LOSS WILD-TYPE   16  290
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 5                 16
  YES              151                290
[1] 2 2
[1] FALSE
D72V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED   105   5   3   4
  18P LOSS WILD-TYPE 213   6   1  15
D72V12, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0              105                213
  R1                5                  6
  R2                3                  1
  RX                4                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     2
  18P LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          10   116
  18P LOSS WILD-TYPE                        16   246
D72V13, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                      10                 16
  WHITE                                         116                246
[1] 4 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     2 109
  18P LOSS WILD-TYPE   5 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2  109
  18P LOSS WILD-TYPE    5  223
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              109                223
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   125  37
  18Q LOSS WILD-TYPE 196  45
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               162                241 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                37                 45 
$`18Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4398 TCGA-05-4405 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
        1523         1431          610          455          365          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
         669          791          791          730          151          882 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 
          30           62          182          264         1147         1492 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2662 
         354         1357          448         1429          400         1280 
TCGA-44-2665 TCGA-44-3918 TCGA-44-6145 TCGA-44-6146 TCGA-44-6775 TCGA-44-6777 
        1301         1036          328          302          705         1942 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-A479 TCGA-44-A47F 
        1978          218         1970          882          486          337 
TCGA-44-A4SU TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-6742 
          76         1421          428          999          157          445 
TCGA-49-6743 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5933 TCGA-50-5941 
         369          944         1499          246         2370          567 
TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-1596 
         686         1015         1986         1971         1178         1375 
TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-7281 
          24           25         1475           67         1233           18 
TCGA-55-7283 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 
          35            4           95           40           39           39 
TCGA-55-7728 TCGA-55-7910 TCGA-55-7994 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
          24          197           31           21            6           43 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8207 TCGA-55-8507 TCGA-55-8616 TCGA-55-A48Z 
           4           15           66            8           48           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-62-8397 TCGA-62-A46U 
          48         1952            1           28         1289         2067 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
        1246          910         1686         1968           62         1305 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6216 
        1559          866           31          610          573          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 TCGA-69-7979 TCGA-69-8254 TCGA-69-A59K 
         422          202          165           89           77          214 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         912          800          131          519         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 
        1956         1965         1973         1988         1950         1963 
TCGA-78-7155 TCGA-78-7161 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-8660 
        1957          215         1972         1949          327         1954 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
         824         1959           11          630         1968         1963 
TCGA-86-8074 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8672 TCGA-91-6829 
          24          476          482           16           15         1940 
TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 
          60          417          372          842          224          492 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-95-7567 TCGA-95-7947 TCGA-97-7547 
          44          218          127          568          477         1965 
TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 
        1932          181           22         1965          147          148 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-MN-A4N4 
         154          114          287          282          578          622 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1967         1951         1954         1970         1955         1971 

$`18Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 
         607          426         1369         1126         1947          578 
TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 
        1958         1997          912          761          761          457 
TCGA-05-5428 TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 
         670           14          225         1952         1962          864 
TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 
        1073         1971          133         1324         1367          741 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
          97          246         1130         1163          190          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6147 TCGA-44-6148 
        1013          863          383          723          845          704 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
         658         1938         1864          444          592          366 
TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         557          535          719          385           99          260 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 
         466          287          351          415         1932         1081 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
         268          896         1700          890          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5930 TCGA-50-5931 
        2174         2146          455          785          282          267 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 
        1091          653          883          764          255          105 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
         424          280          701         1479           87            2 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 
         993         1239         1826         2151         1170          121 
TCGA-55-7570 TCGA-55-7724 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
           6         1958           34           54           19           16 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
          21            3            5           33          100           26 
TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          47           33           46          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          29           11           15          228            9            3 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 
         146          202          536           15           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
         106           33           42            5           47          162 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-64-1676 
        1216         1970         2696         1445         2199         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-67-3773 
         628         1189         1126         1959          864          427 
TCGA-67-3774 TCGA-67-6215 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
         385          174          186          690          414          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 
         184           70          382          100          129           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
        1600          711          467           40          164           38 
TCGA-73-7498 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
         621         1944         1093         1202          760         1948 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
        1961         1963         1221          678         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
        1934         1937         1965         1944          881         1952 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 
         994         1949         1971         1981         1964         1965 
TCGA-80-5608 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
        1972          422          591          508          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8281 TCGA-86-8358 
        1963           13          479          489         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
          26           35           45           34           18          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
         405           10           30           14           39          323 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         310           79           35          197          174           36 
TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7948 
         297          186           34            2          377          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 
         121          964         1332          775          107          182 
TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
          87           15          115          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AG TCGA-L4-A4E6 
         427          459           44          170          238          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 
         116            6          285          353         1946         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH 
        1957         1980         1951         1944         1970          142 
TCGA-MP-A5C7 
        1490 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                  2 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              2370               2696 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             505.5              444.0 
[1] "1.0 - 2370.0 (505.5)" "2.0 - 2696.0 (444.0)"
[1] "hr=" "1"  
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  18Q LOSS MUTATED         1       32       54        22        38         25
  18Q LOSS WILD-TYPE       3       81       77        21        31         42
                    vv
clus                 STAGE IIIB STAGE IV
  18Q LOSS MUTATED            5       13
  18Q LOSS WILD-TYPE          6       10
D73V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 32                 81
  STAGE IB                 54                 77
  STAGE IIA                22                 21
  STAGE IIB                38                 31
  STAGE IIIA               25                 42
  STAGE IIIB                5                  6
  STAGE IV                 13                 10
[1] 8 2
[1] 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    49 116  18   8
  18Q LOSS WILD-TYPE  94 143  22  10
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               49                 94
  T2              116                143
  T3               18                 22
  T4                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                  N0  N1 N2+N3
  18Q LOSS MUTATED   114  45    28
  18Q LOSS WILD-TYPE 181  40    44
D73V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                 114                181
  N1                  45                 40
  N2+N3               28                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  18Q LOSS MUTATED   124  11   0   1  53
  18Q LOSS WILD-TYPE 193   7   1   2  66
D73V6, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               124                193
  M1                11                  7
  M1A                0                  1
  M1B                1                  2
  MX                53                 66
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   114  77
  18Q LOSS WILD-TYPE 134 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    114   77
  18Q LOSS WILD-TYPE  134  137
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              114                134
  MALE                 77                137
[1] 2 2
[1] FALSE
D73V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18Q LOSS MUTATED                            5
  18Q LOSS WILD-TYPE                          8
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18Q LOSS MUTATED                                  40
  18Q LOSS WILD-TYPE                                53
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                  125
  18Q LOSS WILD-TYPE                                                169
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18Q LOSS MUTATED                                            1
  18Q LOSS WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  18Q LOSS MUTATED                                               7
  18Q LOSS WILD-TYPE                                            12
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  18Q LOSS MUTATED                                1
  18Q LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  18Q LOSS MUTATED                                    3
  18Q LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  18Q LOSS MUTATED                              1                             4
  18Q LOSS WILD-TYPE                            1                            15
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  18Q LOSS MUTATED                                 1
  18Q LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  18Q LOSS MUTATED                                               0
  18Q LOSS WILD-TYPE                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  18Q LOSS MUTATED                              3
  18Q LOSS WILD-TYPE                            4
D73V9, multiclass
                                                    clus
vv                                                   18Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              125
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     7
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                     4
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     0
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   18Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                169
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      12
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      15
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       4
  MUCINOUS (COLLOID) CARCINOMA                                        4
[1] 12  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     6 185
  18Q LOSS WILD-TYPE  15 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      6  185
  18Q LOSS WILD-TYPE   15  256
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 6                 15
  YES              185                256
[1] 2 2
[1] FALSE
D73V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   130   8   3   3
  18Q LOSS WILD-TYPE 188   3   1  16
D73V12, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              130                188
  R1                8                  3
  R2                3                  1
  RX                3                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     1
  18Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          11   145
  18Q LOSS WILD-TYPE                        15   217
D73V13, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                      11                 15
  WHITE                                         145                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"
D73V14, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4 129
  18Q LOSS WILD-TYPE   3 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4  129
  18Q LOSS WILD-TYPE    3  203
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              129                203
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED   146  47
  19P LOSS WILD-TYPE 175  35
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               193                210 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                47                 35 
$`19P LOSS MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4410 
         607          426         1369         1947         1431         1958 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 
        1997          912          365          791          761          730 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         457          882          670          225          182          264 
TCGA-38-4625 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
        1952         1492         1073          354         1357          448 
TCGA-44-2655 TCGA-44-2656 TCGA-44-5644 TCGA-44-6144 TCGA-44-6146 TCGA-44-6774 
        1324         1429          863          723          302          658 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
        1938         1864         1978          592          557         1970 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A4SS 
         882          535          385           99          260          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 
          76         1932         1421          428          268          896 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5051 TCGA-50-5072 
         445          369          890          522          455          246 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
         267         1091          567          764          686         1015 
TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
         255          424          280          701         1178         1375 
TCGA-55-5899 TCGA-55-6971 TCGA-55-6972 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 
          87           25         1475            6           40           34 
TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 
         197            3           31            5           33          100 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 
          26            4           23            8           15            3 
TCGA-55-8614 TCGA-55-8616 TCGA-55-A48X TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
         536           48           33         1952           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
          47          162         1216         1289         1970         1445 
TCGA-62-A46U TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
        2067         1246         1728         1968         1959         1305 
TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 TCGA-69-7763 
         864           31          573          385          186          690 
TCGA-69-7764 TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
         414           70          382          129          214           61 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 
         711          800          467          131           38          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
         519         1970         1967         1956         1965         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7156 
        1950         1944         1093         1963          760         1961 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
        1221         1940         1934         1937         1972         1949 
TCGA-78-7539 TCGA-78-7542 TCGA-80-5608 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 
         327         1952         1972           11          422          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
        1963          508           10           13           24          479 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 
         482           16         1955           34           15           10 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
          30          323         1940           60          310          417 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-A4BC TCGA-95-7039 
         372          224           35          492           44           34 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8171 TCGA-97-8174 
           2          568          476          121          107         1965 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 
         392          427          170          154          287          578 
TCGA-L9-A443 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
         116          353         1946         1954         1954         1957 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1944         1970          142         1955         1971 
TCGA-MP-A5C7 
        1490 

$`19P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4424 
        1523         1126          578          610          455          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
         669          791          761          151           30           62 
TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-7271 TCGA-38-A44F 
          14         1962         1147          864         1971          133 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
         400         1367          741         1280         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 
        1013          383          328          845          704          705 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7672 TCGA-44-A479 
        1942          444          366          218          719          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-49-4494 TCGA-49-4506 
         466          287          337          351         1081          999 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
         157         1700          354         2174         2146          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 
         944         1499          282         2370          653          883 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 
         105         1986         1971         1479            2          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
          24         1239           67         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 
        1170           18           35          121            4           95 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1958           39           39           24           54           19 
TCGA-55-7907 TCGA-55-7911 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 
          16           21           21            6           43           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
          15           33           46           66          216           44 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 
          29           11          228            9          146          202 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
          15           49           66          106           42           29 
TCGA-55-A490 TCGA-55-A492 TCGA-62-8399 TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 
          48            1         2696         2199          910          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 
        1189         1686         1126           62         1559          866 
TCGA-67-3771 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         610          427          174          141          422          202 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
         165          230          184           89          100           77 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4675 TCGA-73-4676 TCGA-78-7145 TCGA-78-7152 
        1600          912           40          164         1973         1202 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 
        1948         1957         1963          678          215         1950 
TCGA-78-7220 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1965         1944          881          994         1949         1971 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 
        1981         1954         1964         1965          824         1959 
TCGA-86-7711 TCGA-86-7714 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 
         630         1968          745         1963          489          476 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 
          19           26           35           45           18          455 
TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6847 TCGA-91-8496 
         405           14           39           79          842          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
         174           36          218          297          127          186 
TCGA-95-7944 TCGA-95-7947 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         377          477          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 
         775          181           22          182           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8028 
          15          148          115          197          271          459 
TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 
          44          114          282          238          435            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TE 
         285          622         1967         1951         1980         1970 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                  1 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              2067               2696 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             522.0              413.5 
[1] "2.0 - 2067.0 (522.0)" "1.0 - 2696.0 (413.5)"
[1] "hr=" "1.6"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  19P LOSS MUTATED         3       45       56        24        37         35
  19P LOSS WILD-TYPE       1       68       75        19        32         32
                    vv
clus                 STAGE IIIB STAGE IV
  19P LOSS MUTATED            7       15
  19P LOSS WILD-TYPE          4        8
D74V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   3                  1
  STAGE IA                 45                 68
  STAGE IB                 56                 75
  STAGE IIA                24                 19
  STAGE IIB                37                 32
  STAGE IIIA               35                 32
  STAGE IIIB                7                  4
  STAGE IV                 15                  8
[1] 8 2
[1] 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    62 131  17  10
  19P LOSS WILD-TYPE  81 128  23   8
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               62                 81
  T2              131                128
  T3               17                 23
  T4               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                  N0  N1 N2+N3
  19P LOSS MUTATED   133  48    37
  19P LOSS WILD-TYPE 162  37    35
D74V5, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                 133                162
  N1                  48                 37
  N2+N3               37                 35
[1] 3 2
[1] 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 M1B  MX
  19P LOSS MUTATED   160  12   1   2  45
  19P LOSS WILD-TYPE 157   6   0   1  74
D74V6, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               160                157
  M1                12                  6
  M1A                1                  0
  M1B                2                  1
  MX                45                 74
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   105 117
  19P LOSS WILD-TYPE 143  97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    105  117
  19P LOSS WILD-TYPE  143   97
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE              105                143
  MALE                117                 97
[1] 2 2
[1] FALSE
D74V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19P LOSS MUTATED                            5
  19P LOSS WILD-TYPE                          8
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19P LOSS MUTATED                                  49
  19P LOSS WILD-TYPE                                44
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                  142
  19P LOSS WILD-TYPE                                                152
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19P LOSS MUTATED                                            0
  19P LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  19P LOSS MUTATED                                               9
  19P LOSS WILD-TYPE                                            10
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  19P LOSS MUTATED                                1
  19P LOSS WILD-TYPE                              1
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  19P LOSS MUTATED                                    2
  19P LOSS WILD-TYPE                                  2
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  19P LOSS MUTATED                              1                             9
  19P LOSS WILD-TYPE                            1                            10
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  19P LOSS MUTATED                                 0
  19P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  19P LOSS MUTATED                                               1
  19P LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  19P LOSS MUTATED                              3
  19P LOSS WILD-TYPE                            4
D74V9, multiclass
                                                    clus
vv                                                   19P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              142
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     9
  LUNG CLEAR CELL ADENOCARCINOMA                                    1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                2
  LUNG MUCINOUS ADENOCARCINOMA                                      1
  LUNG PAPILLARY ADENOCARCINOMA                                     9
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   19P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  44
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                152
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      10
  LUNG CLEAR CELL ADENOCARCINOMA                                      1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  2
  LUNG MUCINOUS ADENOCARCINOMA                                        1
  LUNG PAPILLARY ADENOCARCINOMA                                      10
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        4
[1] 12  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     7 215
  19P LOSS WILD-TYPE  14 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7  215
  19P LOSS WILD-TYPE   14  226
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 7                 14
  YES              215                226
[1] 2 2
[1] FALSE
D74V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED   153   2   3  10
  19P LOSS WILD-TYPE 165   9   1   9
D74V12, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0              153                165
  R1                2                  9
  R2                3                  1
  RX               10                  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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  1     4
  19P LOSS WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                          13   169
  19P LOSS WILD-TYPE                        13   193
D74V13, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  2
  BLACK OR AFRICAN AMERICAN                      13                 13
  WHITE                                         169                193
[1] 4 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     3 155
  19P LOSS WILD-TYPE   4 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3  155
  19P LOSS WILD-TYPE    4  177
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              155                177
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    89  30
  19Q LOSS WILD-TYPE 232  52
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               119                284 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                30                 52 
$`19Q LOSS MUTATED`
TCGA-05-4396 TCGA-05-4398 TCGA-05-4410 TCGA-05-4415 TCGA-05-4420 TCGA-05-4432 
        1947         1431         1958         1997          912          761 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-38-4625 TCGA-38-4630 TCGA-38-4632 
         457          882          670         1952         1073         1357 
TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 TCGA-44-5644 TCGA-44-6778 TCGA-44-6779 
         448         1324         1429          863         1864         1978 
TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         557          882          535          385           99          260 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4505 TCGA-49-4507 TCGA-49-6742 TCGA-49-6745 
          76         1932          428          268          445          522 
TCGA-50-5051 TCGA-50-5072 TCGA-50-5932 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
         455          246         1091          567          764          686 
TCGA-50-6597 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
        1015          424          701         1178         1375           87 
TCGA-55-6972 TCGA-55-7570 TCGA-55-7727 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        1475            6           34           31            5           33 
TCGA-55-8507 TCGA-55-8511 TCGA-55-8616 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DG 
           8            9           48           33         1952          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 
        1216         1289         1445         1246         1728         1968 
TCGA-67-3770 TCGA-67-3772 TCGA-69-7978 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
          31          573           70          129          214           61 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         711          800          131           38          621          519 
TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
        1970         1956         1965         1988         1944         1093 
TCGA-78-7153 TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 
         760         1940         1937         1972         1949         1952 
TCGA-86-7701 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8074 TCGA-86-8075 
          11          591         1963          508           24          479 
TCGA-86-8279 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 
         482           34           15           10           30          323 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 
        1940          310          417          372          224           35 
TCGA-91-7771 TCGA-91-A4BC TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-97-8171 
         492           44           34          568          476          107 
TCGA-99-7458 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-MP-A4SV 
         392          170          154          287          578         1946 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1957         1951         1955         1971         1490 

$`19Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4403 
        1523          607          426         1369         1126          578 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
         610          455          365          913          669          791 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
         791          761          730          151           30           62 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
          14          225          182          264         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 
        1492          864          354         1971          133          400 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        1367          741         1280         1301           97          246 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1130         1163         1036          190          722         1013 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
         383          723          328          302          845          704 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 
         658          705         1938         1942          444          592 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A 
         366          218         1970          719          486          466 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4494 TCGA-49-4501 
         287          337          351          415         1081         1421 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
         999          896          157         1700          369          890 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
         354         2174         2146          785          944         1499 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 TCGA-50-7109 
         282          267         2370          653          883          255 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 
         105         1986         1971          280         1479            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 
         993           24         1239           25           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1233         2151         1170           18           35          121 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40         1958           39           39 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          24           54           19           16          197           21 
TCGA-55-7914 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
           3           21          100            6           43           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
           4           47           15           33           46           66 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
         216           44           23           29           11           15 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
         228            3          146          202          536           15 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          49           66          106           42           29           48 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8399 
           1           28            5           47         1970         2696 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        2067         2199          910          628         1189         1686 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
        1126         1959           62         1305          864         1559 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         866          610          427          385          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         422          202          186          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         230          184           89          382          100           77 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-75-7025 
        1600          912          467           40          164         1967 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 
        1973         1950         1963         1202         1948         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 
        1961         1963         1221          678          215         1950 
TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1934         1965         1944          327          881          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
        1949         1971         1981         1954         1964         1965 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1972          824         1959          630          422         1968 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
         745           10         1963           13          489          476 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
          16         1955           19           26           35           45 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 
          18          455          405           14           39           60 
TCGA-91-6835 TCGA-91-6847 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
          79          842          197          174           36          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 
         297          127          186            2          377          477 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         121          964         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
         181           22          182         1965           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 
          15          148          115          197          271          427 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
         459           44          114          282          238          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
         116            6          285          622          353         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE 
        1951         1954         1954         1980         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TH 
        1970          142 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                  1 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1997               2696 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             568.0              418.5 
[1] "5.0 - 1997.0 (568.0)" "1.0 - 2696.0 (418.5)"
[1] "hr=" "1.5"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  19Q LOSS MUTATED         1       28       35        11        26         23
  19Q LOSS WILD-TYPE       3       85       96        32        43         44
                    vv
clus                 STAGE IIIB STAGE IV
  19Q LOSS MUTATED            7       11
  19Q LOSS WILD-TYPE          4       12
D75V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 28                 85
  STAGE IB                 35                 96
  STAGE IIA                11                 32
  STAGE IIB                26                 43
  STAGE IIIA               23                 44
  STAGE IIIB                7                  4
  STAGE IV                 11                 12
[1] 8 2
[1] 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    36  83  13   9
  19Q LOSS WILD-TYPE 107 176  27   9
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               36                107
  T2               83                176
  T3               13                 27
  T4                9                  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
  19Q LOSS MUTATED    85  30    25
  19Q LOSS WILD-TYPE 210  55    47
D75V5, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                  85                210
  N1                  30                 55
  N2+N3               25                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  19Q LOSS MUTATED   102  10   1   0  27
  19Q LOSS WILD-TYPE 215   8   0   3  92
D75V6, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               102                215
  M1                10                  8
  M1A                1                  0
  M1B                0                  3
  MX                27                 92
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    70  72
  19Q LOSS WILD-TYPE 178 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     70   72
  19Q LOSS WILD-TYPE  178  142
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               70                178
  MALE                 72                142
[1] 2 2
[1] FALSE
D75V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19Q LOSS MUTATED                            2
  19Q LOSS WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19Q LOSS MUTATED                                  32
  19Q LOSS WILD-TYPE                                61
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                   92
  19Q LOSS WILD-TYPE                                                202
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19Q LOSS MUTATED                                            0
  19Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  19Q LOSS MUTATED                                               5
  19Q LOSS WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  19Q LOSS MUTATED                                0
  19Q LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  19Q LOSS MUTATED                                    1
  19Q LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  19Q LOSS MUTATED                              0                             7
  19Q LOSS WILD-TYPE                            2                            12
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  19Q LOSS MUTATED                                 0
  19Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  19Q LOSS MUTATED                                               2
  19Q LOSS WILD-TYPE                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  19Q LOSS MUTATED                              1
  19Q LOSS WILD-TYPE                            6
D75V9, multiclass
                                                    clus
vv                                                   19Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               92
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     7
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     2
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   19Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                202
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      12
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       2
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     4 138
  19Q LOSS WILD-TYPE  17 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4  138
  19Q LOSS WILD-TYPE   17  303
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 4                 17
  YES              138                303
[1] 2 2
[1] FALSE
D75V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    95   2   3   5
  19Q LOSS WILD-TYPE 223   9   1  14
D75V12, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               95                223
  R1                2                  9
  R2                3                  1
  RX                5                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     4
  19Q LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           7   107
  19Q LOSS WILD-TYPE                        19   255
D75V13, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  2
  BLACK OR AFRICAN AMERICAN                       7                 19
  WHITE                                         107                255
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2  99
  19Q LOSS WILD-TYPE   5 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   99
  19Q LOSS WILD-TYPE    5  233
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               99                233
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    65  23
  20P LOSS WILD-TYPE 256  59
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                88                315 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                23                 59 
$`20P LOSS MUTATED`
TCGA-05-4405 TCGA-05-4415 TCGA-05-4422 TCGA-05-5423 TCGA-05-5428 TCGA-44-2656 
         610         1997          365          151          670         1429 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3919 TCGA-44-6779 TCGA-44-A47A 
        1280         1301          246          190         1978          466 
TCGA-44-A47G TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-49-6743 TCGA-49-6745 
         351         1421          428          157          369          522 
TCGA-50-5051 TCGA-50-5072 TCGA-50-5933 TCGA-50-5944 TCGA-50-6597 TCGA-53-7624 
         455          246         2370          764         1015         1986 
TCGA-55-1594 TCGA-55-1595 TCGA-55-6712 TCGA-55-6980 TCGA-55-7725 TCGA-55-7727 
        1178         1479           24           67           39           34 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7994 TCGA-55-8090 TCGA-55-8092 TCGA-55-8207 
          19           16           31            6           26           66 
TCGA-55-8506 TCGA-55-8616 TCGA-62-8397 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
          11           48         1289         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1681 TCGA-64-5781 TCGA-67-3770 
         910         1728         1189         1968         1559           31 
TCGA-67-3773 TCGA-67-6216 TCGA-69-7761 TCGA-69-7974 TCGA-69-A59K TCGA-73-4666 
         427          141          186          184          214          800 
TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-75-6214 TCGA-78-7145 TCGA-78-7146 
         131           40          519         1970         1973         1988 
TCGA-78-7148 TCGA-78-7158 TCGA-78-7535 TCGA-78-7537 TCGA-78-8660 TCGA-86-6851 
        1944         1963         1972         1944         1954         1959 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8280 TCGA-86-8673 TCGA-91-6828 TCGA-91-6831 
         591          508           16          455          323          310 
TCGA-91-6835 TCGA-91-6848 TCGA-93-7347 TCGA-95-7039 TCGA-95-7043 TCGA-97-8177 
          79          224          297           34            2          147 
TCGA-99-7458 TCGA-99-8033 TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MP-A4SV 
         392          170          578            6          622         1946 
TCGA-MP-A4SW TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TI 
        1967         1957         1944         1955 

$`20P LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 
        1523          607          426         1369         1126         1947 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 
        1431          578         1958          455          912          913 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
         669          791          791          761          761          730 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         457          882           30           62           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         182          264         1952         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         864         1073          354         1357          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 
         133         1324          400         1367          741           97 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
        1130         1163         1036          722         1013          863 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
         383          723          328          302          845          704 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
         658          705         1938         1942         1864          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         592          366          218          557         1970          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
         535          719          385           99          260          486 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         287          337          415           76         1932         1081 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
         999          268          896         1700          445          890 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
         354         2174         2146          785          944         1499 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         282          267         1091          653          567          883 
TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
         686          255          105         1971          424          280 
TCGA-55-1592 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 
         701         1375           87            2          993         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
          25         1475         1826         1233         2151         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
          18           35          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 
          40         1958           39           24           54          197 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
          21            3            5           33           21          100 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
          43            4           47           15           33           46 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
         216           44           23           29            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
          15           49           66          106           33           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          29           48         1952            1           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
          47          162         1216         1970         2696         1445 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
         628         1686         1126         1959           62         1305 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 
         864          866          610          573          385          174 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
         422          202          690          414          165          230 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
          70           89          382          100           77          129 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 
          61         1600          711          912          467          164 
TCGA-73-4677 TCGA-73-7498 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7147 
          38          621         1967         1956         1965         1950 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1093         1963         1202          760         1948         1957 
TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1961         1221          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 
        1934         1937         1965         1949          327          881 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
        1952          994         1949         1971         1981         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
        1965         1972          824           11          630          422 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
        1968         1963          745           10         1963           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 
          24          479          489          476          482         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
          19           26           35           45           34           18 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
          15          405           10           30           14           39 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
        1940           60          417          372          842           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          197          174           36           44          218 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
         127          186          568          377          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         121          964         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
         181           22          107          182         1965           87 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 
          15          148          115          197          271          427 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
         459           44          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T2 
         238          435          116          285          353         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1954         1980         1951         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1971         1490 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                  1 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              2370               2696 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               487                459 
[1] "2.0 - 2370.0 (487.0)" "1.0 - 2696.0 (459.0)"
[1] "hr=" "1.2"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  20P LOSS MUTATED         1       19       30         9        18         21
  20P LOSS WILD-TYPE       3       94      101        34        51         46
                    vv
clus                 STAGE IIIB STAGE IV
  20P LOSS MUTATED            4        6
  20P LOSS WILD-TYPE          7       17
D76V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   1                  3
  STAGE IA                 19                 94
  STAGE IB                 30                101
  STAGE IIA                 9                 34
  STAGE IIB                18                 51
  STAGE IIIA               21                 46
  STAGE IIIB                4                  7
  STAGE IV                  6                 17
[1] 8 2
[1] 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    27  63  10   6
  20P LOSS WILD-TYPE 116 196  30  12
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1               27                116
  T2               63                196
  T3               10                 30
  T4                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                  N0  N1 N2+N3
  20P LOSS MUTATED    64  20    23
  20P LOSS WILD-TYPE 231  65    49
D76V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                  64                231
  N1                  20                 65
  N2+N3               23                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  20P LOSS MUTATED    81   6   0   0  21
  20P LOSS WILD-TYPE 236  12   1   3  98
D76V6, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                81                236
  M1                 6                 12
  M1A                0                  1
  M1B                0                  3
  MX                21                 98
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    57  51
  20P LOSS WILD-TYPE 191 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     57   51
  20P LOSS WILD-TYPE  191  163
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               57                191
  MALE                 51                163
[1] 2 2
[1] FALSE
D76V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20P LOSS MUTATED                            3
  20P LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20P LOSS MUTATED                                  26
  20P LOSS WILD-TYPE                                67
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                   67
  20P LOSS WILD-TYPE                                                227
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20P LOSS MUTATED                                            0
  20P LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20P LOSS MUTATED                                               5
  20P LOSS WILD-TYPE                                            14
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  20P LOSS MUTATED                                2
  20P LOSS WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  20P LOSS MUTATED                                    1
  20P LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  20P LOSS MUTATED                              0                             2
  20P LOSS WILD-TYPE                            2                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  20P LOSS MUTATED                                 0
  20P LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  20P LOSS MUTATED                                               1
  20P LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  20P LOSS MUTATED                              1
  20P LOSS WILD-TYPE                            6
D76V9, multiclass
                                                    clus
vv                                                   20P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               67
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     5
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   20P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  67
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                227
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      14
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     4 104
  20P LOSS WILD-TYPE  17 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4  104
  20P LOSS WILD-TYPE   17  337
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 4                 17
  YES              104                337
[1] 2 2
[1] FALSE
D76V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    79   3   1   3
  20P LOSS WILD-TYPE 239   8   3  16
D76V12, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               79                239
  R1                3                  8
  R2                1                  3
  RX                3                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     1
  20P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           2    87
  20P LOSS WILD-TYPE                        24   275
D76V13, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       2                 24
  WHITE                                          87                275
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  76
  20P LOSS WILD-TYPE   6 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   76
  20P LOSS WILD-TYPE    6  256
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               76                256
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    41  12
  20Q LOSS WILD-TYPE 280  70
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                53                350 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                12                 70 
$`20Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4405 TCGA-05-4415 TCGA-05-4422 TCGA-05-5428 TCGA-44-2656 
        1523          610         1997          365          670         1429 
TCGA-44-2662 TCGA-44-3919 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4501 
        1280          190          466          287          351         1421 
TCGA-49-6743 TCGA-49-6745 TCGA-50-5051 TCGA-50-5072 TCGA-53-7624 TCGA-53-A4EZ 
         369          522          455          246         1986          280 
TCGA-55-1595 TCGA-55-8087 TCGA-55-8090 TCGA-55-8097 TCGA-55-8207 TCGA-62-8397 
        1479           21            6           15           66         1289 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-67-3770 TCGA-67-3773 
        2067          910         1728         1189           31          427 
TCGA-67-6216 TCGA-69-7761 TCGA-69-A59K TCGA-73-4675 TCGA-73-7499 TCGA-78-7146 
         141          186          214           40          519         1988 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7537 TCGA-86-6851 TCGA-86-7953 TCGA-86-7955 
        1963          678         1944         1959          591          508 
TCGA-86-8280 TCGA-86-8358 TCGA-91-6828 TCGA-91-6831 TCGA-93-7347 TCGA-97-8174 
          16           19          323          310          297         1965 
TCGA-99-7458 TCGA-99-8033 TCGA-MP-A4SW TCGA-MP-A4TC TCGA-MP-A4TI 
         392          170         1967         1944         1955 

$`20Q LOSS WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
         607          426         1369         1126         1947         1431 
TCGA-05-4403 TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 
         578         1958          455          912          913          669 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
         791          791          761          761          730          457 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         151          882           30           62           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         182          264         1952         1962         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         864         1073          354         1357          448         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 
         133         1324          400         1367          741         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 
          97          246         1130         1163         1036          722 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
        1013          863          383          723          328          302 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         845          704          658          705         1938         1942 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
        1864         1978          444          592          366          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         557         1970          882          535          719          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU 
          99          260          486          337          415           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        1932         1081          428          999          268          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6761 TCGA-50-5045 
         157         1700          445          890          354         2174 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
        2146          785          944         1499          282          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1091         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
         686         1015          255          105         1971          424 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         701         1178         1375           87            2          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
          24         1239           25         1475           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1233         2151         1170           18           35          121 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
           6            4           95           40         1958           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
          39           34           24           54           19           16 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
         197           21            3           31            5           33 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 
         100           43           26            4           47           33 
TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          46          216           44           23           29           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
           8           15          228            9            3          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         202          536           15           48           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
         106           33           42           29           48         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
           1           28            5           47          162         1216 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1677 
        1970         2696         1445         2199         1246          628 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1686         1126         1968         1959           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 
         864         1559          866          610          573          385 
TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         174          422          202          690          414          165 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
         230          184           70           89          382          100 
TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
          77          129           61         1600          711          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         800          467          131          164           38          621 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 
        1970         1967         1956         1965         1973         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1944         1093         1963         1202          760         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1957         1961         1221          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
        1934         1937         1965         1972         1949          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         881         1952          994         1949         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 
        1954         1964         1965         1972          824           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
         630          422         1968         1963          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        1963           13           24          479          489          476 
TCGA-86-8279 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
         482         1955           26           35           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          18           15          455          405           10           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
          14           39         1940           60           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         372          842          224           35          492          197 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 
         174           36           44          218          127          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
          34            2          568          377          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         121          964         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 
         181           22          107          182           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 
          15          148          115          197          271          427 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
         459           44          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         238          578          435          116            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
         622          353         1946         1951         1954         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1957         1980         1951         1970         1970          142 
TCGA-MP-A4TK TCGA-MP-A5C7 
        1971         1490 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                  1 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2067               2696 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
               508                458 
[1] "6.0 - 2067.0 (508.0)" "1.0 - 2696.0 (458.0)"
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  20Q LOSS MUTATED         0       11       24         8         5         10
  20Q LOSS WILD-TYPE       4      102      107        35        64         57
                    vv
clus                 STAGE IIIB STAGE IV
  20Q LOSS MUTATED            2        4
  20Q LOSS WILD-TYPE          9       19
D77V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  4
  STAGE IA                 11                102
  STAGE IB                 24                107
  STAGE IIA                 8                 35
  STAGE IIB                 5                 64
  STAGE IIIA               10                 57
  STAGE IIIB                2                  9
  STAGE IV                  4                 19
[1] 8 2
[1] 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    16  39   4   4
  20Q LOSS WILD-TYPE 127 220  36  14
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1               16                127
  T2               39                220
  T3                4                 36
  T4                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                  N0  N1 N2+N3
  20Q LOSS MUTATED    43   8    11
  20Q LOSS WILD-TYPE 252  77    61
D77V5, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                  43                252
  N1                   8                 77
  N2+N3               11                 61
[1] 3 2
[1] 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 M1B  MX
  20Q LOSS MUTATED    51   4   0   0   9
  20Q LOSS WILD-TYPE 266  14   1   3 110
D77V6, multiclass
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                51                266
  M1                 4                 14
  M1A                0                  1
  M1B                0                  3
  MX                 9                110
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    33  31
  20Q LOSS WILD-TYPE 215 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     33   31
  20Q LOSS WILD-TYPE  215  183
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               33                215
  MALE                 31                183
[1] 2 2
[1] FALSE
D77V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20Q LOSS MUTATED                            3
  20Q LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20Q LOSS MUTATED                                  17
  20Q LOSS WILD-TYPE                                76
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q LOSS MUTATED                                                   34
  20Q LOSS WILD-TYPE                                                260
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20Q LOSS MUTATED                                            0
  20Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20Q LOSS MUTATED                                               3
  20Q LOSS WILD-TYPE                                            16
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  20Q LOSS MUTATED                                2
  20Q LOSS WILD-TYPE                              0
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  20Q LOSS MUTATED                                    1
  20Q LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  20Q LOSS MUTATED                              0                             2
  20Q LOSS WILD-TYPE                            2                            17
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  20Q LOSS MUTATED                                 0
  20Q LOSS WILD-TYPE                               1
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  20Q LOSS MUTATED                                               1
  20Q LOSS WILD-TYPE                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  20Q LOSS MUTATED                              1
  20Q LOSS WILD-TYPE                            6
D77V9, multiclass
                                                    clus
vv                                                   20Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               34
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     3
  LUNG CLEAR CELL ADENOCARCINOMA                                    2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     2
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   20Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                260
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      16
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      17
  LUNG SIGNET RING ADENOCARCINOMA                                     1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       3
  MUCINOUS (COLLOID) CARCINOMA                                        6
[1] 12  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     1  63
  20Q LOSS WILD-TYPE  20 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   63
  20Q LOSS WILD-TYPE   20  378
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 1                 20
  YES               63                378
[1] 2 2
[1] FALSE
D77V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED    47   1   1   4
  20Q LOSS WILD-TYPE 271  10   3  15
D77V12, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               47                271
  R1                1                 10
  R2                1                  3
  RX                4                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     1
  20Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           1    51
  20Q LOSS WILD-TYPE                        25   311
D77V13, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                       1                 25
  WHITE                                          51                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"
D77V14, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2  44
  20Q LOSS WILD-TYPE   5 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2   44
  20Q LOSS WILD-TYPE    5  288
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               44                288
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   105  31
  21Q LOSS WILD-TYPE 216  51
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               136                267 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                31                 51 
$`21Q LOSS MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
        1523          607         1369         1126         1947         1431 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4430 
         455          912          365          913          791          761 
TCGA-05-4432 TCGA-05-5420 TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 TCGA-38-4627 
         761          457           30          225          182         1147 
TCGA-44-2659 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6778 
        1367         1013          863          723          328         1864 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 
        1978          592          366          218          557          882 
TCGA-44-7672 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-49-4506 
         719          486          287          337          415          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5051 
         268          896          522          354         2174          455 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5944 
        1499          246         1091         2370          653          764 
TCGA-50-5946 TCGA-50-7109 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
         686          255          424          701         1178         1375 
TCGA-55-5899 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
          87           25         1475         1826         1233         2151 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 
          40         1958           24           54          197           21 
TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8205 TCGA-55-8302 
          31          100            6           26           33           23 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8514 TCGA-55-A490 TCGA-55-A491 
           8           15          228          202           48         1952 
TCGA-55-A4DF TCGA-62-8402 TCGA-62-A471 TCGA-64-1677 TCGA-64-1679 TCGA-64-5774 
          47         1445         1246          628         1686         1959 
TCGA-64-5775 TCGA-64-5781 TCGA-67-3770 TCGA-69-7760 TCGA-69-7761 TCGA-69-7974 
          62         1559           31          202          186          184 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
          89          382          129         1600          711          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
         467          131           40         1956         1965         1988 
TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 TCGA-78-7159 TCGA-78-7167 TCGA-78-7220 
        1944          760         1948         1221         1937         1965 
TCGA-78-7536 TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-86-7701 TCGA-86-7713 
        1949         1949         1954         1972           11          422 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-91-6828 
         591          745           26           35           34          323 
TCGA-91-6840 TCGA-91-7771 TCGA-95-7043 TCGA-97-7547 TCGA-97-8172 TCGA-97-8174 
         372          492            2         1965          182         1965 
TCGA-97-8175 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AE 
          87          427          459           44          170          282 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4TE TCGA-MP-A4TF 
         622         1946         1970         1970 

$`21Q LOSS WILD-TYPE`
TCGA-05-4384 TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4425 
         426          578          610         1958         1997          669 
TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 
         791          730          151          882          670           62 
TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4628 TCGA-38-4629 
          14          264         1952         1962         1492          864 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
        1073          354         1357          448         1971          133 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        1324         1429          400          741         1280         1301 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
          97          246         1130         1163         1036          190 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         722          383          302          845          704          658 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7669 TCGA-44-7671 
         705         1938         1942          444         1970          535 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SU 
         385           99          260          466          351           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-49-4514 
        1932         1081         1421          428          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         445          369          890         2146          785          944 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5941 TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 
         282          267          567          883         1015          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 
        1986         1971          280         1479            2          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
          24         1239           67         1170           18           35 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 
         121            6            4           95           39           39 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
          34           19           16            3            5           33 
TCGA-55-8087 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
          21           43            4           47           15           46 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8511 
          66          216           44           29           11            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
           3          146          536           15           48           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A492 
          66          106           33           42           29            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
          28            5          162         1216         1289         1970 
TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
        2696         2067         2199          910         1728         1189 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 
        1126         1968         1305          864          866          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         573          427          385          174          141          422 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-8253 
         690          414          165          230           70          100 
TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 TCGA-73-4676 TCGA-73-4677 
          77          214           61          912          164           38 
TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 
         621          519         1970         1967         1973         1950 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1093         1963         1202         1957         1961         1963 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
         678          215         1940         1950         1934         1972 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
        1944          327          881         1952          994         1971 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 
        1981         1964         1965          824         1959          630 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
        1968         1963          508           10         1963           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
          24          479          489          476          482           16 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1955           19           45           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
         405           10           30           14           39         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
          60          310           79          417          842          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
          35          197          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
         297          127          186           34          568          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 
         477          476          121          964         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8177 TCGA-97-8179 
         775          181           22          107          147           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-J2-8192 
         148          115          197          271          392          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         114          287          238          578          435          116 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
           6          285          353         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH 
        1954         1957         1980         1951         1944          142 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                  1 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              2370               2696 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             591.5              428.0 
[1] "2.0 - 2370.0 (591.5)" "1.0 - 2696.0 (428.0)"
[1] "hr=" "1.2"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  21Q LOSS MUTATED         2       34       42        11        25         23
  21Q LOSS WILD-TYPE       2       79       89        32        44         44
                    vv
clus                 STAGE IIIB STAGE IV
  21Q LOSS MUTATED            5        7
  21Q LOSS WILD-TYPE          6       16
D78V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   2                  2
  STAGE IA                 34                 79
  STAGE IB                 42                 89
  STAGE IIA                11                 32
  STAGE IIB                25                 44
  STAGE IIIA               23                 44
  STAGE IIIB                5                  6
  STAGE IV                  7                 16
[1] 8 2
[1] 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    41  87  13   6
  21Q LOSS WILD-TYPE 102 172  27  12
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               41                102
  T2               87                172
  T3               13                 27
  T4                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                  N0  N1 N2+N3
  21Q LOSS MUTATED    97  26    23
  21Q LOSS WILD-TYPE 198  59    49
D78V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                  97                198
  N1                  26                 59
  N2+N3               23                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  21Q LOSS MUTATED   105   7   0   0  36
  21Q LOSS WILD-TYPE 212  11   1   3  83
D78V6, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               105                212
  M1                 7                 11
  M1A                0                  1
  M1B                0                  3
  MX                36                 83
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    72  77
  21Q LOSS WILD-TYPE 176 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     72   77
  21Q LOSS WILD-TYPE  176  137
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               72                176
  MALE                 77                137
[1] 2 2
[1] FALSE
D78V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  21Q LOSS MUTATED                            7
  21Q LOSS WILD-TYPE                          6
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  21Q LOSS MUTATED                                  24
  21Q LOSS WILD-TYPE                                69
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                  103
  21Q LOSS WILD-TYPE                                                191
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  21Q LOSS MUTATED                                            0
  21Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  21Q LOSS MUTATED                                               2
  21Q LOSS WILD-TYPE                                            17
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  21Q LOSS MUTATED                                0
  21Q LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  21Q LOSS MUTATED                                    1
  21Q LOSS WILD-TYPE                                  3
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  21Q LOSS MUTATED                              0                             5
  21Q LOSS WILD-TYPE                            2                            14
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  21Q LOSS MUTATED                                 1
  21Q LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  21Q LOSS MUTATED                                               3
  21Q LOSS WILD-TYPE                                             1
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  21Q LOSS MUTATED                              3
  21Q LOSS WILD-TYPE                            4
D78V9, multiclass
                                                    clus
vv                                                   21Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              103
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     2
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                1
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     5
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   21Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                191
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      17
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  3
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      14
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       1
  MUCINOUS (COLLOID) CARCINOMA                                        4
[1] 12  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    10 139
  21Q LOSS WILD-TYPE  11 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     10  139
  21Q LOSS WILD-TYPE   11  302
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                10                 11
  YES              139                302
[1] 2 2
[1] FALSE
D78V11, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED   102   2   1   4
  21Q LOSS WILD-TYPE 216   9   3  15
D78V12, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              102                216
  R1                2                  9
  R2                1                  3
  RX                4                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     1
  21Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          11   109
  21Q LOSS WILD-TYPE                        15   253
D78V13, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                      11                 15
  WHITE                                         109                253
[1] 4 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     2 103
  21Q LOSS WILD-TYPE   5 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2  103
  21Q LOSS WILD-TYPE    5  229
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              103                229
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   139  32
  22Q LOSS WILD-TYPE 182  50
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               171                232 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                32                 50 
$`22Q LOSS MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4415 TCGA-05-4424 TCGA-05-4426 
        1369         1126         1947         1997          913          791 
TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 
         791          761          730          457          882          670 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4628 TCGA-38-6178 TCGA-44-2656 
         225          182          264         1492          448         1429 
TCGA-44-2659 TCGA-44-2662 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1367         1280         1036          190          722         1013 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6778 TCGA-44-7667 
         863          723          328          845         1864          557 
TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS TCGA-49-4501 TCGA-49-4505 
         535          385          260          415         1421          428 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-6744 TCGA-49-6761 TCGA-50-5051 
         999          268          896          890          354          455 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-6597 
         282         1091         2370          653          567         1015 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6642 
         255         1986          424          280           87          993 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 
          25         1475           67         1233           18           35 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
           6           95           40           19          197           21 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8205 TCGA-55-8207 TCGA-55-8505 TCGA-55-8507 
          26            4           33           66           29            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8615 TCGA-55-8616 
          15          228            9            3           15           48 
TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
          66           29           48           28           47          162 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
        2067          910         1728          628         1686         1968 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-6217 TCGA-69-7760 
        1959         1305          864         1559          422          202 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
         186          690          414          230           70           89 
TCGA-69-7980 TCGA-69-8253 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 
         382          100          214           61          711          912 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 
         467          131           38         1970         1956         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7152 TCGA-78-7159 TCGA-78-7163 TCGA-78-7167 
        1973         1988         1202         1221         1950         1937 
TCGA-78-7535 TCGA-78-7536 TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-83-5908 
        1972         1949         1949         1954         1972          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 
        1959           11          630          591         1963          745 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 
        1963           24          479          482           19           26 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8672 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 
          35           34           15           30          323         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-7771 TCGA-91-8499 
          60          310          417          372          492           36 
TCGA-91-A4BC TCGA-95-7039 TCGA-95-7567 TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 
          44           34          568          964         1932          775 
TCGA-97-7937 TCGA-97-8175 TCGA-97-8547 TCGA-99-7458 TCGA-99-8032 TCGA-J2-A4AG 
         181           87          148          392           44          238 
TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T8 
         578            6          353         1946         1951         1957 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF 
        1951         1970         1970 

$`22Q LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        1523          607          426         1431          578          610 
TCGA-05-4410 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4430 
        1958          455          912          365          669          761 
TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 
         151           30           62           14         1952         1962 
TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 
        1147          864         1073          354         1357         1971 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 
         133         1324          400          741         1301           97 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-5645 TCGA-44-6146 TCGA-44-6148 
         246         1130         1163          383          302          704 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
         658          705         1938         1942         1978          444 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 
         592          366          218         1970          882          719 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
          99          486          466          287          337          351 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
          76         1932         1081          157         1700          445 
TCGA-49-6743 TCGA-49-6745 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         369          522         2174         2146          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        1499          246          267          883          764          686 
TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
         105         1971          701         1178         1479         1375 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 
           2           24         1239         1826         2151         1170 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
         121            4         1958           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          24           54           16            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 
          33           21          100            6           43           47 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
          15           46          216           44           23           11 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
         146          202          536           49          106           33 
TCGA-55-A48Y TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 
          42         1952            1            5         1216         1289 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 TCGA-64-1678 
        1970         2696         1445         2199         1246         1189 
TCGA-64-1680 TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1126           62          866           31          610          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7765 TCGA-69-7974 
         427          385          174          141          165          184 
TCGA-69-8254 TCGA-69-8255 TCGA-73-4658 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 
          77          129         1600          800           40          164 
TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
         621          519         1967         1950         1944         1093 
TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
        1963          760         1948         1957         1961         1963 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 
         678          215         1940         1934         1965         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
         327          881         1952          994         1971         1981 
TCGA-78-8662 TCGA-80-5607 TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 TCGA-86-8055 
        1964         1965          422         1968          508           10 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 
          13          489          476           16         1955           45 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
          18          455          405           10           14           39 
TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
          79          842          224           35          197          174 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7944 
         218          297          127          186            2          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7553 TCGA-97-7941 
         477          476          121         1965         1332           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
         107          182         1965          147           15          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 
         197          271          427          459          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A443 TCGA-MN-A4N1 
         114          287          282          435          116          285 
TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC 
         622         1967         1954         1954         1980         1944 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         1490 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                  1 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              2370               2696 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               479                457 
[1] "3.0 - 2370.0 (479.0)" "1.0 - 2696.0 (457.0)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  22Q LOSS MUTATED         3       44       54        17        31         31
  22Q LOSS WILD-TYPE       1       69       77        26        38         36
                    vv
clus                 STAGE IIIB STAGE IV
  22Q LOSS MUTATED            6       11
  22Q LOSS WILD-TYPE          5       12
D79V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   3                  1
  STAGE IA                 44                 69
  STAGE IB                 54                 77
  STAGE IIA                17                 26
  STAGE IIB                31                 38
  STAGE IIIA               31                 36
  STAGE IIIB                6                  5
  STAGE IV                 11                 12
[1] 8 2
[1] 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    61 111  17   8
  22Q LOSS WILD-TYPE  82 148  23  10
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               61                 82
  T2              111                148
  T3               17                 23
  T4                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                  N0  N1 N2+N3
  22Q LOSS MUTATED   126  36    33
  22Q LOSS WILD-TYPE 169  49    39
D79V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                 126                169
  N1                  36                 49
  N2+N3               33                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  22Q LOSS MUTATED   137   8   0   3  47
  22Q LOSS WILD-TYPE 180  10   1   0  72
D79V6, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               137                180
  M1                 8                 10
  M1A                0                  1
  M1B                3                  0
  MX                47                 72
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    96 101
  22Q LOSS WILD-TYPE 152 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     96  101
  22Q LOSS WILD-TYPE  152  113
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               96                152
  MALE                101                113
[1] 2 2
[1] FALSE
D79V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  22Q LOSS MUTATED                            8
  22Q LOSS WILD-TYPE                          5
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  22Q LOSS MUTATED                                  36
  22Q LOSS WILD-TYPE                                57
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                  127
  22Q LOSS WILD-TYPE                                                167
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  22Q LOSS MUTATED                                            1
  22Q LOSS WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  22Q LOSS MUTATED                                              10
  22Q LOSS WILD-TYPE                                             9
                    vv
clus                 LUNG CLEAR CELL ADENOCARCINOMA
  22Q LOSS MUTATED                                0
  22Q LOSS WILD-TYPE                              2
                    vv
clus                 LUNG MICROPAPILLARY ADENOCARCINOMA
  22Q LOSS MUTATED                                    3
  22Q LOSS WILD-TYPE                                  1
                    vv
clus                 LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  22Q LOSS MUTATED                              0                             6
  22Q LOSS WILD-TYPE                            2                            13
                    vv
clus                 LUNG SIGNET RING ADENOCARCINOMA
  22Q LOSS MUTATED                                 1
  22Q LOSS WILD-TYPE                               0
                    vv
clus                 LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  22Q LOSS MUTATED                                               3
  22Q LOSS WILD-TYPE                                             1
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  22Q LOSS MUTATED                              2
  22Q LOSS WILD-TYPE                            5
D79V9, multiclass
                                                    clus
vv                                                   22Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                36
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              127
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    10
  LUNG CLEAR CELL ADENOCARCINOMA                                    0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                3
  LUNG MUCINOUS ADENOCARCINOMA                                      0
  LUNG PAPILLARY ADENOCARCINOMA                                     6
  LUNG SIGNET RING ADENOCARCINOMA                                   1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     3
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   22Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  57
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                167
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                       9
  LUNG CLEAR CELL ADENOCARCINOMA                                      2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      13
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                       1
  MUCINOUS (COLLOID) CARCINOMA                                        5
[1] 12  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     8 189
  22Q LOSS WILD-TYPE  13 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      8  189
  22Q LOSS WILD-TYPE   13  252
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 8                 13
  YES              189                252
[1] 2 2
[1] FALSE
D79V11, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED   136   5   1   6
  22Q LOSS WILD-TYPE 182   6   3  13
D79V12, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0              136                182
  R1                5                  6
  R2                1                  3
  RX                6                 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                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     1
  22Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          11   153
  22Q LOSS WILD-TYPE                        15   209
D79V13, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  5
  BLACK OR AFRICAN AMERICAN                      11                 15
  WHITE                                         153                209
[1] 4 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     3 144
  22Q LOSS WILD-TYPE   4 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3  144
  22Q LOSS WILD-TYPE    4  188
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              144                188
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    41  10
  XQ LOSS WILD-TYPE 280  72
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               51               352 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               10                72 
$`XQ LOSS MUTATED`
TCGA-05-4396 TCGA-05-4405 TCGA-05-5428 TCGA-05-5715 TCGA-44-5643 TCGA-44-6146 
        1947          610          670           62         1013          302 
TCGA-44-8120 TCGA-49-4507 TCGA-50-5066 TCGA-50-5932 TCGA-50-6597 TCGA-50-7109 
         260          268          944         1091         1015          255 
TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-7570 TCGA-55-7576 TCGA-55-7903 
         701         1479         1375            6           40           19 
TCGA-55-8090 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A4DG TCGA-62-8397 TCGA-62-A46U 
           6           29         1952          162         1289         2067 
TCGA-62-A472 TCGA-64-5778 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-69-7764 
         910         1305          866          573          427          414 
TCGA-69-7973 TCGA-73-4670 TCGA-73-7499 TCGA-78-7146 TCGA-78-7166 TCGA-78-7220 
         230          131          519         1988         1934         1965 
TCGA-78-7536 TCGA-78-7542 TCGA-78-8655 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
        1949         1952         1981         1963          508          745 
TCGA-86-8281 TCGA-86-8359 TCGA-91-8496 TCGA-95-7039 TCGA-95-7567 TCGA-97-8172 
        1955           26          197           34          568          182 
TCGA-97-8547 TCGA-97-A4M7 TCGA-MP-A4TK 
         148          271         1971 

$`XQ LOSS WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
        1523          607          426         1369         1126         1431 
TCGA-05-4403 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
         578         1958         1997          455          912          365 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
         913          669          791          791          761          761 
TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-35-3615 
         730          457          151          882           30           14 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
         225          182          264         1952         1962         1147 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
        1492          864         1073          354         1357          448 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
        1971          133         1324         1429          400         1367 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         741         1280         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 
        1163         1036          190          722          863          383 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
         723          328          845          704          658          705 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
        1938         1942         1864         1978          444          592 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
         366          218          557         1970          882          535 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
         719          385           99          486          466          287 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
         337          351          415           76         1932         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
        1421          428          999          896          157         1700 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 
         445          369          890          522          354         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
        2146          455          785         1499          246          282 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
         267         2370          653          567          883          764 
TCGA-50-5946 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
         686          105         1986         1971          424          280 
TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
        1178           87            2          993           24         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
          25         1475           67         1826         1233         2151 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 
        1170           18           35          121            4           95 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        1958           39           39           34           24           54 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          16          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
          33           21          100           43           26            4 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
          47           15           33           46           66          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          44           23           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
          15           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          42           48            1           28            5           47 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 
        1216         1970         2696         1445         2199         1246 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        1728          628         1189         1686         1126         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 
        1959           62          864         1559           31          610 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         690          165          184           70           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
         100           77          129          214           61         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
         711          912          800          467           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
          38          621         1970         1967         1956         1965 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1973         1950         1944         1093         1963         1202 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
         760         1948         1957         1961         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 
         678          215         1940         1950         1937         1972 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1944          327          881          994         1949         1971 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1954         1964         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8055 
          11          630          422         1968          591           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        1963           13           24          479          489          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
         482           16           19           35           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          18           15          455          405           10           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          14           39          323         1940           60          310 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
          79          417          372          842          224           35 
TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         492          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
         127          186            2          377          477          476 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         121          964         1965         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
         181           22          107         1965           87          147 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
          15          115          197          392          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
          44          170          154          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
         238          578          435          116            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         622          353         1946         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1970          142         1955         1490 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6                 1 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2067              2696 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              610               455 
[1] "6.0 - 2067.0 (610.0)" "1.0 - 2696.0 (455.0)"
[1] "hr=" "1.3"
D80V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  XQ LOSS MUTATED         1       11       18         1        12          8
  XQ LOSS WILD-TYPE       3      102      113        42        57         59
                   vv
clus                STAGE IIIB STAGE IV
  XQ LOSS MUTATED            3        2
  XQ LOSS WILD-TYPE          8       21
D80V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  1                 3
  STAGE IA                11               102
  STAGE IB                18               113
  STAGE IIA                1                42
  STAGE IIB               12                57
  STAGE IIIA               8                59
  STAGE IIIB               3                 8
  STAGE IV                 2                21
[1] 8 2
[1] 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    14  34   6   2
  XQ LOSS WILD-TYPE 129 225  34  16
D80V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              14               129
  T2              34               225
  T3               6                34
  T4               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                 N0  N1 N2+N3
  XQ LOSS MUTATED    34  11     9
  XQ LOSS WILD-TYPE 261  74    63
D80V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0                 34               261
  N1                 11                74
  N2+N3               9                63
[1] 3 2
[1] 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 M1B  MX
  XQ LOSS MUTATED    44   2   0   0  10
  XQ LOSS WILD-TYPE 273  16   1   3 109
D80V6, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               44               273
  M1                2                16
  M1A               0                 1
  M1B               0                 3
  MX               10               109
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    26  30
  XQ LOSS WILD-TYPE 222 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     26   30
  XQ LOSS WILD-TYPE  222  184
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              26               222
  MALE                30               184
[1] 2 2
[1] FALSE
D80V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XQ LOSS MUTATED                            2
  XQ LOSS WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XQ LOSS MUTATED                                  19
  XQ LOSS WILD-TYPE                                74
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                   28
  XQ LOSS WILD-TYPE                                                266
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  XQ LOSS MUTATED                                            0
  XQ LOSS WILD-TYPE                                          4
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  XQ LOSS MUTATED                                               3
  XQ LOSS WILD-TYPE                                            16
                   vv
clus                LUNG CLEAR CELL ADENOCARCINOMA
  XQ LOSS MUTATED                                1
  XQ LOSS WILD-TYPE                              1
                   vv
clus                LUNG MICROPAPILLARY ADENOCARCINOMA
  XQ LOSS MUTATED                                    1
  XQ LOSS WILD-TYPE                                  3
                   vv
clus                LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  XQ LOSS MUTATED                              1                             0
  XQ LOSS WILD-TYPE                            1                            19
                   vv
clus                LUNG SIGNET RING ADENOCARCINOMA
  XQ LOSS MUTATED                                 0
  XQ LOSS WILD-TYPE                               1
                   vv
clus                LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  XQ LOSS MUTATED                                               0
  XQ LOSS WILD-TYPE                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  XQ LOSS MUTATED                              1
  XQ LOSS WILD-TYPE                            6
D80V9, multiclass
                                                    clus
vv                                                   XQ LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              28
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                    3
  LUNG CLEAR CELL ADENOCARCINOMA                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                               1
  LUNG MUCINOUS ADENOCARCINOMA                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                    0
  LUNG SIGNET RING ADENOCARCINOMA                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                    0
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   XQ LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               266
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     16
  LUNG CLEAR CELL ADENOCARCINOMA                                     1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                 3
  LUNG MUCINOUS ADENOCARCINOMA                                       1
  LUNG PAPILLARY ADENOCARCINOMA                                     19
  LUNG SIGNET RING ADENOCARCINOMA                                    1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                      4
  MUCINOUS (COLLOID) CARCINOMA                                       6
[1] 12  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     5  51
  XQ LOSS WILD-TYPE  16 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      5   51
  XQ LOSS WILD-TYPE   16  390
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                5                16
  YES              51               390
[1] 2 2
[1] FALSE
D80V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    37   0   0   1
  XQ LOSS WILD-TYPE 281  11   4  18
D80V12, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              37               281
  R1               0                11
  R2               0                 4
  RX               1                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                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     2
  XQ LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           5    42
  XQ LOSS WILD-TYPE                        21   320
D80V13, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 4
  BLACK OR AFRICAN AMERICAN                      5                21
  WHITE                                         42               320
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  44
  XQ LOSS WILD-TYPE   7 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   44
  XQ LOSS WILD-TYPE    7  288
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              44               288
[1] 2 2
[1] FALSE
