[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/11541582/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/11548106/transformed.cor.cli.txt"

nPatients in clinical file=483, in cluster file=515, common to both=476
[1]  80 476
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              130               346 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              130               346 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              282               194 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              282               194 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              147               329 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              147               329 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              132               344 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              132               344 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               39               437 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               39               437 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               84               392 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               84               392 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               80               396 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               80               396 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               45               431 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               45               431 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              258               218 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              258               218 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              117               359 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              117               359 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              132               344 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              132               344 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               56               420 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               56               420 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              250               226 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              250               226 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              205               271 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              205               271 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              117               359 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              117               359 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              229               247 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              229               247 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               45               431 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               45               431 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               33               443 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               33               443 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               107                369 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               107                369 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                77                399 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                77                399 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                91                385 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                91                385 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               112                364 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               112                364 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               132                344 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               132                344 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               125                351 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               125                351 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                42                434 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                42                434 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               115                361 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               115                361 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                37                439 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                37                439 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               121                355 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               121                355 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                93                383 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                93                383 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                79                397 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                79                397 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               180                296 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               180                296 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                90                386 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                90                386 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                66                410 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                66                410 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                31                445 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                31                445 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                71                405 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                71                405 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               161                315 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               161                315 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               186                290 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               186                290 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                87                389 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                87                389 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                61                415 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                61                415 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               72               404 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               72               404 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               77               399 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               77               399 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               449 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               27               449 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               23               453 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               23               453 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               23               453 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               23               453 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              199               277 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              199               277 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              137               339 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              137               339 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              110               366 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              110               366 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              125               351 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              125               351 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               38               438 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               38               438 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              132               344 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              132               344 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               98               378 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               98               378 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              201               275 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              201               275 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               32               444 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               32               444 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               38               438 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               38               438 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              188               288 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              188               288 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               51               425 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               51               425 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              245               231 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              245               231 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              231               245 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              231               245 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               104                372 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               104                372 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               124                352 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               124                352 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               108                368 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               108                368 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                86                390 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                86                390 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               102                374 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               102                374 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                91                385 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                91                385 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               229                247 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               229                247 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               107                369 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               107                369 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               226                250 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               226                250 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               107                369 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               107                369 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               134                342 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               134                342 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               204                272 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               204                272 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                57                419 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                57                419 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               163                313 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               163                313 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               197                279 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               197                279 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               225                251 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               225                251 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               145                331 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               145                331 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               111                365 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               111                365 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                65                411 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                65                411 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               154                322 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               154                322 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               203                273 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               203                273 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               59               417 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               59               417 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "COMPLETENESS.OF.RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 476 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-49-AARQ TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
        6443           NA         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-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        2370          653           NA           NA          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
         764          686           NA           NA           NA           NA 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 
          NA           NA         1015           NA          255          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
          NA           NA          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-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
          NA         1239           NA           25         1475           NA 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
          NA           NA           67           NA           NA         1826 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
          NA         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          705 
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          462          100            6          600           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8204 TCGA-55-8205 TCGA-55-8206 
           4           47           15           NA           33           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          66          674          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 
          NA            1           28            5           47          162 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
          NA         1216         1289           NA         2696         1445 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
          NA           NA           NA           NA         2067         2199 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
          NA           NA         1246          910         1728          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
        1189         1686         1126           NA         2676           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-67-4679 TCGA-67-6215 TCGA-67-6216 
         573          427          385           NA          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-73-4675 TCGA-73-4676 
         912          800          467          131           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5122 TCGA-75-5125 
          38          621          519          305           NA           NA 
TCGA-75-5126 TCGA-75-5146 TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 TCGA-75-6206 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
          NA           NA           NA           NA           NA           NA 
TCGA-75-7030 TCGA-75-7031 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
          NA         1093           NA         1202          760           NA 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
          NA           NA           NA         1221          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
          NA         6812           NA           NA           NA           NA 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
          NA           NA          327          881           NA          994 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
        6346           NA         2360           NA           NA           NA 
TCGA-80-5608 TCGA-80-5611 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
          NA           NA          824           NA           NA           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
         630          422           NA          591           NA          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
         745           10           NA           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           NA           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-A4JF TCGA-86-A4P7 
         455          405           10           30           NA           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          39          323           NA           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 
         505          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
         127          186           34            2           NA          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
         377          477          476          830           84          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         553          605          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
         775          181           NA           22          107          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
          NA           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-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         170          154          114          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
         578          435          116            6          266           NA 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         312          111          102          827         1175           84 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
          NA           NA          142           NA           NA           NA 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 
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=123,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=291,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=23,	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=93,	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=26,	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 476 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 
147 267  42  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
147 267  42  18 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
147 267  42  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
147 267  42  18 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
301  91  72   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  301    91    74 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
301  91  72   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  301    91    74 
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=93, 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    88  28
  1P GAIN WILD-TYPE 241  59
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              116               300 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               28                59 
$`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-44-7660 TCGA-44-7662 
        1280          705         1864         1978          592          218 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8119 TCGA-44-A47B TCGA-44-A4SU TCGA-49-4501 
        1970          719           99          287           76         1421 
TCGA-49-4505 TCGA-49-4510 TCGA-49-6742 TCGA-49-6744 TCGA-49-AARQ TCGA-50-5045 
         428          896          445          890         6443         2174 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 
        1499          246          267         2370          567          764 
TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 
         686         1015          701           24         1239           67 
TCGA-55-6983 TCGA-55-7281 TCGA-55-7573 TCGA-55-7576 TCGA-55-7911 TCGA-55-8089 
        1826           18            4           40           21          100 
TCGA-55-8096 TCGA-55-8206 TCGA-55-8514 TCGA-55-A48X TCGA-55-A494 TCGA-55-A4DF 
          47           46          202           33            5           47 
TCGA-55-A4DG TCGA-62-8399 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5781 
         162         2696         1728         1686         1968         1559 
TCGA-67-3772 TCGA-67-6217 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
         573          422          382          100           77          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-75-7025 
         214           61          467          131          164         1967 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 TCGA-78-7161 
        1965         1973         1950         1948         1957          215 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        1940         1937         1972         1952          994         1949 
TCGA-78-8655 TCGA-86-7953 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
        1981          591           10           24          479          482 
TCGA-86-8280 TCGA-86-8585 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6828 
          16           35          455           10           14          323 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 
         310          372          842           34         1973          377 
TCGA-95-8494 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8177 TCGA-97-8552 
          84          964         1332          181          147          115 
TCGA-99-7458 TCGA-J2-A4AG TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MP-A4SW 
         392          238          312          111          827         1967 
TCGA-MP-A4TC TCGA-MP-A4TF 
        1944         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-44-7661 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 
         444          366          557          882          535          385 
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          705           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          462            6          600 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 
          26            4           15           33           66          674 
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-55-8614 
          15          228            9            3          146          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y 
          15           48           49           66          106           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-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1289         1970         1445         2067         2199         1246 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 
         910          628         1189         1126         1959           62 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 
        1305          864          866           31          610          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-73-A9RS TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 
         621          519          305         1970         1956         1988 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
        1944         1093         1963         1202          760         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
        1963         1221          678         1950         1934         1965 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8648 TCGA-78-8660 
        1949         1944          327          881         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          505          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-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
         568          477          476          830          121          553 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 
         605         1965         1932          775           22          107 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 
         182         1965           87           15          148          197 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         271          427          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         114          287          282          578          435          116 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
           6          266          102         1175           84         1946 
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-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970          142         1955         1971         1490          121 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                 1 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             6443              2199 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            524.5             464.0 
[1] "4.0 - 6443.0 (524.5)" "1.0 - 2199.0 (464.0)"
[1] "hr=" "1.1"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  1P GAIN MUTATED         3       29       36        18        21         14
  1P GAIN WILD-TYPE       2       87       96        31        49         54
                   vv
clus                STAGE IIIB STAGE IV
  1P GAIN MUTATED            2        6
  1P GAIN WILD-TYPE          9       18
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                29                87
  STAGE IB                36                96
  STAGE IIA               18                31
  STAGE IIB               21                49
  STAGE IIIA              14                54
  STAGE IIIB               2                 9
  STAGE IV                 6                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
  1P GAIN MUTATED    40  78   8   4
  1P GAIN WILD-TYPE 107 189  34  14
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              40               107
  T2              78               189
  T3               8                34
  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    78  36    14
  1P GAIN WILD-TYPE 223  55    60
D1V5, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0                 78               223
  N1                 36                55
  N2+N3              14                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
  1P GAIN MUTATED    93   6   0   0  29
  1P GAIN WILD-TYPE 233  12   1   4  94
D1V6, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               93               233
  M1                6                12
  M1A               0                 1
  M1B               0                 4
  MX               29                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"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    69  61
  1P GAIN WILD-TYPE 186 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     69   61
  1P GAIN WILD-TYPE  186  160
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              69               186
  MALE                61               160
[1] 2 2
[1] FALSE
D1V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1P GAIN MUTATED                            2
  1P GAIN WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1P GAIN MUTATED                                  21
  1P GAIN WILD-TYPE                                73
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                   90
  1P GAIN WILD-TYPE                                                213
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1P GAIN MUTATED                                            0
  1P GAIN WILD-TYPE                                          5
                   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                                             3
                   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                               21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              90
  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                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               213
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      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"
D1V10, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     4 126
  1P GAIN WILD-TYPE  17 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4  126
  1P GAIN WILD-TYPE   17  329
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                4                17
  YES             126               329
[1] 2 2
[1] FALSE
D1V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    84   4   1   4
  1P GAIN WILD-TYPE 243   8   3  17
D1V12, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              84               243
  R1               4                 8
  R2               1                 3
  RX               4                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
  1P GAIN MUTATED                                  1     2
  1P GAIN WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          14    97
  1P GAIN WILD-TYPE                        21   270
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                     14                21
  WHITE                                         97               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"
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2  88
  1P GAIN WILD-TYPE   5 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   88
  1P GAIN WILD-TYPE    5  257
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              88               257
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   202  49
  1Q GAIN WILD-TYPE 127  38
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              251               165 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               49                38 
$`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-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 
        1978          444          592          218         1970          882 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B 
         535          719          385           99          466          287 
TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4501 
         337          415           76         1932         1081         1421 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
         428          999          896          445          369          890 
TCGA-49-AARQ TCGA-50-5045 TCGA-50-5051 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
        6443         2174          455         1499          246          267 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
        2370          653          567          764          686         1015 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1596 TCGA-55-6642 
         105         1971          424          701         1375          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6987 
          24         1239         1475           67         1826         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          18           35          121            4           95           40 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
          39           34           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          462          100 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8301 TCGA-55-8506 
          26            4           47           46           44           11 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
          15          228            9          202           15           48 
TCGA-55-8619 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
          49           33           42           29         1952            1 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 TCGA-64-1676 
           5           47          162         1970         2696         1728 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 
        1686         1126         1968          864         1559          610 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         573          385          174          422          202          186 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
         414          165          230           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-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
         912          467          131           40          164           38 
TCGA-73-7498 TCGA-73-A9RS TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 
         621          305         1967         1965         1973         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
        1944         1093         1963          760         1948         1961 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 
        1963         1221          678          215         1940         1937 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 
        1972         1944          327          994         1949         1981 
TCGA-80-5608 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
        1972          422          591         1963          745           10 
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-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          26           35           34          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
          30           14          323          310           79          372 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-93-7348 TCGA-93-8067 
         842           35          492          505          127          186 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 
          34         1973          568          377          477          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
          84          121          553          605          964         1965 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8177 TCGA-97-8179 
        1332          775          181          182          147           15 
TCGA-97-8552 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
         115          271          392           44          170          114 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV 
         287          238          116            6          312          111 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 
         827         1175           84         1946         1967         1954 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-S2-AA1A 
        1944         1970          142         1490          121 

$`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-44-7661 TCGA-44-7667 TCGA-44-8120 
         302          704          658          366          557          260 
TCGA-44-A479 TCGA-44-A47G TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6745 
         486          351          268          157         1700          522 
TCGA-49-6761 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5932 
         354         2146          785          944          282         1091 
TCGA-50-5942 TCGA-50-7109 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
         883          255         1986          280         1178         1479 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6971 TCGA-55-6985 TCGA-55-6986 TCGA-55-7570 
          87            2           25         1233         2151            6 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7728 TCGA-55-7994 TCGA-55-8090 TCGA-55-8091 
         705           39           24           31            6          600 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
          15           33           66          674          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-86-7701 
        1954         1964         1965          824         1959           11 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8278 
         630         1968          508         1963           13          476 
TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-A4P8 TCGA-91-6829 
          19           45           18           15           39         1940 
TCGA-91-6830 TCGA-91-6836 TCGA-91-6848 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          60          417          224          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-95-7043 TCGA-95-7948 TCGA-97-7552 TCGA-97-7941 
         218          297            2          476         1932           22 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M2 TCGA-99-8025 
         107         1965           87          148          197          427 
TCGA-99-8028 TCGA-J2-8192 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
         459          154          282          578          435          266 
TCGA-L9-A8F4 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
         102         1951         1954         1957         1980         1951 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1970         1955         1971 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                 2 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             6443              2199 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              455               557 
[1] "1.0 - 6443.0 (455.0)" "2.0 - 2199.0 (557.0)"
[1] "hr=" "1"  
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  1Q GAIN MUTATED         3       73       78        31        41         34
  1Q GAIN WILD-TYPE       2       43       54        18        29         34
                   vv
clus                STAGE IIIB STAGE IV
  1Q GAIN MUTATED            8       13
  1Q GAIN WILD-TYPE          3       11
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                73                43
  STAGE IB                78                54
  STAGE IIA               31                18
  STAGE IIB               41                29
  STAGE IIIA              34                34
  STAGE IIIB               8                 3
  STAGE IV                13                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
  1Q GAIN MUTATED    89 154  26  12
  1Q GAIN WILD-TYPE  58 113  16   6
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              89                58
  T2             154               113
  T3              26                16
  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   179  56    38
  1Q GAIN WILD-TYPE 122  35    36
D2V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                179               122
  N1                 56                35
  N2+N3              38                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
  1Q GAIN MUTATED   193  11   0   1  74
  1Q GAIN WILD-TYPE 133   7   1   3  49
D2V6, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              193               133
  M1               11                 7
  M1A               0                 1
  M1B               1                 3
  MX               74                49
[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   144 138
  1Q GAIN WILD-TYPE 111  83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    144  138
  1Q GAIN WILD-TYPE  111   83
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE             144               111
  MALE               138                83
[1] 2 2
[1] FALSE
D2V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1Q GAIN MUTATED                           12
  1Q GAIN WILD-TYPE                          3
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1Q GAIN MUTATED                                  53
  1Q GAIN WILD-TYPE                                41
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                  178
  1Q GAIN WILD-TYPE                                                125
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1Q GAIN MUTATED                                            1
  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                                               4
  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                                      12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             178
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  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                    4
  MUCINOUS (COLLOID) CARCINOMA                                     4
                                                    clus
vv                                                   1Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 41
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               125
  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    10 272
  1Q GAIN WILD-TYPE  11 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     10  272
  1Q GAIN WILD-TYPE   11  183
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               10                11
  YES             272               183
[1] 2 2
[1] FALSE
D2V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED   188   8   2  15
  1Q GAIN WILD-TYPE 139   4   2   6
D2V12, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             188               139
  R1               8                 4
  R2               2                 2
  RX              15                 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                          23   219
  1Q GAIN WILD-TYPE                        12   148
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                     23                12
  WHITE                                        219               148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     3 205
  1Q GAIN WILD-TYPE   4 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3  205
  1Q GAIN WILD-TYPE    4  140
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             205               140
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED   106  21
  2P GAIN WILD-TYPE 223  66
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              127               289 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               21                66 
$`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-49-AARQ TCGA-50-5072 
         896          445          369          890         6443          246 
TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         686         1015         1986          424          280          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 
        1178         1479         1375         1826           18           35 
TCGA-55-7573 TCGA-55-7576 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 
           4           40           16          197           21            5 
TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 
          47           33          674            8          228            9 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
          15           48           66           28            5          162 
TCGA-62-8402 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-67-3770 TCGA-67-6217 
        1445         1189         1126         1959           31          422 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 
         414          230          184           70          382          129 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-75-6214 
         912          467           40          164          305         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7149 TCGA-78-7155 
        1967         1956         1965         1973         1093         1957 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7220 TCGA-78-7539 
        1221          678          215         1950         1965          327 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-7711 
         994         1949         1981         1964         1972          630 
TCGA-86-7713 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8359 TCGA-86-8585 
         422          508          745           10           26           35 
TCGA-86-8669 TCGA-86-8673 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          34          455         1940          310           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VK 
         372          842            2          568          377          121 
TCGA-97-7547 TCGA-97-8179 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
        1965           15          427           44          170          114 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T9 TCGA-MP-A4TC 
         116            6          827           84         1980         1944 
TCGA-MP-A4TK 
        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          705           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          462          100            6          600 
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-78-7535 TCGA-78-7536 TCGA-78-7537 
        1940         1934         1937         1972         1949         1944 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 TCGA-83-5908 
         881         1952         1971         1954         1965          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8056 
        1959           11         1968          591         1963         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-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
          16         1955           19           45           18           15 
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-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
          60          224           35          492          505          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-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
          34         1973          477          476          830           84 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         553          605          964         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-99-8028 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
         459          154          287          282          238          578 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
         435          266          312          111          102         1175 
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-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1951         1970         1970          142         1955         1490 
TCGA-S2-AA1A 
         121 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                 1 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             6443              2696 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              448               486 
[1] "2.0 - 6443.0 (448.0)" "1.0 - 2696.0 (486.0)"
[1] "hr=" "1.5"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  2P GAIN MUTATED         2       37       37        16        18         24
  2P GAIN WILD-TYPE       3       79       95        33        52         44
                   vv
clus                STAGE IIIB STAGE IV
  2P GAIN MUTATED            4        9
  2P GAIN WILD-TYPE          7       15
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                37                79
  STAGE IB                37                95
  STAGE IIA               16                33
  STAGE IIB               18                52
  STAGE IIIA              24                44
  STAGE IIIB               4                 7
  STAGE IV                 9                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    43  80  16   6
  2P GAIN WILD-TYPE 104 187  26  12
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              43               104
  T2              80               187
  T3              16                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    87  30    27
  2P GAIN WILD-TYPE 214  61    47
D3V5, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0                 87               214
  N1                 30                61
  N2+N3              27                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   102   7   0   2  35
  2P GAIN WILD-TYPE 224  11   1   2  88
D3V6, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              102               224
  M1                7                11
  M1A               0                 1
  M1B               2                 2
  MX               35                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"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    83  64
  2P GAIN WILD-TYPE 172 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     83   64
  2P GAIN WILD-TYPE  172  157
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              83               172
  MALE                64               157
[1] 2 2
[1] FALSE
D3V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2P GAIN MUTATED                            3
  2P GAIN WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2P GAIN MUTATED                                  34
  2P GAIN WILD-TYPE                                60
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                   94
  2P GAIN WILD-TYPE                                                209
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2P GAIN MUTATED                                            0
  2P GAIN WILD-TYPE                                          5
                   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                                             3
                   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                               34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              94
  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                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               209
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      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"
D3V10, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     6 141
  2P GAIN WILD-TYPE  15 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      6  141
  2P GAIN WILD-TYPE   15  314
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                6                15
  YES             141               314
[1] 2 2
[1] FALSE
D3V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED   105   7   2   6
  2P GAIN WILD-TYPE 222   5   2  15
D3V12, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0             105               222
  R1               7                 5
  R2               2                 2
  RX               6                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
  2P GAIN MUTATED                                  1     2
  2P GAIN WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           9   109
  2P GAIN WILD-TYPE                        26   258
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                      9                26
  WHITE                                        109               258
[1] 4 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  99
  2P GAIN WILD-TYPE   2 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5   99
  2P GAIN WILD-TYPE    2  246
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO              99               246
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    96  19
  2Q GAIN WILD-TYPE 233  68
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              115               301 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19                68 
$`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-49-AARQ TCGA-50-5072 TCGA-50-6597 
         896          445          890         6443          246         1015 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
        1986          424          280          701         1178         1375 
TCGA-55-6983 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7726 
        1826           18           35            4           40           39 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8096 TCGA-55-8205 
          16          197           21            5           47           33 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 
          66          674            8          228          202           15 
TCGA-55-8620 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8402 TCGA-62-A471 
          66           28            5          162         1445         1246 
TCGA-64-1680 TCGA-67-3770 TCGA-67-3771 TCGA-67-6217 TCGA-69-7764 TCGA-69-7973 
        1126           31          610          422          414          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 TCGA-73-4662 TCGA-73-4675 
         184           70          382          129          912           40 
TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7149 
         305         1970         1967         1956         1965         1093 
TCGA-78-7155 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
        1957          678         1940         1950         1937         1965 
TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
         327          994         1949         1981         1964         1972 
TCGA-86-6851 TCGA-86-7713 TCGA-86-8055 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
        1959          422           10           26           35           34 
TCGA-86-8673 TCGA-91-6829 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
         455         1940           79          417          372          842 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-97-7547 TCGA-97-8179 TCGA-99-8025 
           2          568          377         1965           15          427 
TCGA-99-8033 TCGA-J2-8194 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T9 
         170          114            6          827           84         1980 
TCGA-MP-A4TC 
        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          705           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          462          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 
           6          600           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 
         505          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
         127          186           34         1973          477          476 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
         830           84          121          553          605          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-97-8174 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-J2-8192 
         197          271          392          459           44          154 
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-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV 
         266          312          111          102         1175         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA 
        1967         1951         1954         1954         1957         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 
TCGA-S2-AA1A 
         121 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                 1 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             6443              2696 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              445               486 
[1] "2.0 - 6443.0 (445.0)" "1.0 - 2696.0 (486.0)"
[1] "hr=" "1.4"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  2Q GAIN MUTATED         2       33       34        14        15         22
  2Q GAIN WILD-TYPE       3       83       98        35        55         46
                   vv
clus                STAGE IIIB STAGE IV
  2Q GAIN MUTATED            4        8
  2Q GAIN WILD-TYPE          7       16
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                33                83
  STAGE IB                34                98
  STAGE IIA               14                35
  STAGE IIB               15                55
  STAGE IIIA              22                46
  STAGE IIIB               4                 7
  STAGE IV                 8                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    38  73  14   5
  2Q GAIN WILD-TYPE 109 194  28  13
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              38               109
  T2              73               194
  T3              14                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    79  27    24
  2Q GAIN WILD-TYPE 222  64    50
D4V5, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0                 79               222
  N1                 27                64
  N2+N3              24                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  2Q GAIN MUTATED    92   6   0   2  31
  2Q GAIN WILD-TYPE 234  12   1   2  92
D4V6, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               92               234
  M1                6                12
  M1A               0                 1
  M1B               2                 2
  MX               31                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"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    70  62
  2Q GAIN WILD-TYPE 185 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     70   62
  2Q GAIN WILD-TYPE  185  159
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              70               185
  MALE                62               159
[1] 2 2
[1] FALSE
D4V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2Q GAIN MUTATED                            3
  2Q GAIN WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2Q GAIN MUTATED                                  34
  2Q GAIN WILD-TYPE                                60
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                   81
  2Q GAIN WILD-TYPE                                                222
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2Q GAIN MUTATED                                            0
  2Q GAIN WILD-TYPE                                          5
                   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                                             3
                   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)              81
  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                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               222
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      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"
D4V10, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     5 127
  2Q GAIN WILD-TYPE  16 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5  127
  2Q GAIN WILD-TYPE   16  328
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                5                16
  YES             127               328
[1] 2 2
[1] FALSE
D4V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    97   5   2   4
  2Q GAIN WILD-TYPE 230   7   2  17
D4V12, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              97               230
  R1               5                 7
  R2               2                 2
  RX               4                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
  2Q GAIN MUTATED                                  0     1
  2Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                          11    95
  2Q GAIN WILD-TYPE                        24   272
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                     11                24
  WHITE                                         95               272
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     4  90
  2Q GAIN WILD-TYPE   3 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   90
  2Q GAIN WILD-TYPE    3  255
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO              90               255
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    28   6
  3P GAIN WILD-TYPE 301  81
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               34               382 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                81 
$`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-49-AARQ TCGA-50-5946 TCGA-53-A4EZ 
         287          268          369         6443          686          280 
TCGA-55-6972 TCGA-55-7903 TCGA-55-7995 TCGA-55-8208 TCGA-64-1677 TCGA-64-5775 
        1475           19            5          674          628           62 
TCGA-69-7760 TCGA-69-7974 TCGA-69-7978 TCGA-69-A59K TCGA-73-4676 TCGA-78-7145 
         202          184           70          214          164         1973 
TCGA-78-8662 TCGA-86-7711 TCGA-86-7953 TCGA-86-8074 TCGA-86-8075 TCGA-91-6828 
        1964          630          591           24          479          323 
TCGA-95-8494 TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 
          84          287          116            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          705 
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          462 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
         100            6          600           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-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
         621          519          305         1970         1967         1956 
TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1965         1988         1950         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-78-7540 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-86-6851 TCGA-86-7701 
        1954         1965         1972          824         1959           11 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
         422         1968         1963          508          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        1963           13          489          476          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-A456 TCGA-86-A4D0 
          18           15          455          405           10           30 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          14           39         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 
         505          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
         127          186           34            2         1973          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
         377          477          476          830          121          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         605          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-97-8177 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-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
         114          282          238          578          435          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         312          111          102          827         1175           84 
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-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 TCGA-S2-AA1A 
        1955         1971         1490          121 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                 1 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             6443              2696 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            305.0             479.5 
[1] "5.0 - 6443.0 (305.0)" "1.0 - 2696.0 (479.5)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  3P GAIN MUTATED         1       11        7         6         6          6
  3P GAIN WILD-TYPE       4      105      125        43        64         62
                   vv
clus                STAGE IIIB STAGE IV
  3P GAIN MUTATED            0        2
  3P GAIN WILD-TYPE         11       22
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                11               105
  STAGE IB                 7               125
  STAGE IIA                6                43
  STAGE IIB                6                64
  STAGE IIIA               6                62
  STAGE IIIB               0                11
  STAGE IV                 2                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
  3P GAIN MUTATED    14  18   4   3
  3P GAIN WILD-TYPE 133 249  38  15
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              14               133
  T2              18               249
  T3               4                38
  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    23  12     4
  3P GAIN WILD-TYPE 278  79    70
D5V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                 23               278
  N1                 12                79
  N2+N3               4                70
[1] 3 2
[1] 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    26   2   0   0  11
  3P GAIN WILD-TYPE 300  16   1   4 112
D5V6, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               26               300
  M1                2                16
  M1A               0                 1
  M1B               0                 4
  MX               11               112
[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    21  18
  3P GAIN WILD-TYPE 234 203
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     21   18
  3P GAIN WILD-TYPE  234  203
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              21               234
  MALE                18               203
[1] 2 2
[1] FALSE
D5V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3P GAIN MUTATED                            2
  3P GAIN WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3P GAIN MUTATED                                  10
  3P GAIN WILD-TYPE                                84
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                   24
  3P GAIN WILD-TYPE                                                279
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3P GAIN MUTATED                                            0
  3P GAIN WILD-TYPE                                          5
                   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                                             5
                   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)              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                                    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                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               279
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      5
  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  36
  3P GAIN WILD-TYPE  18 419
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   36
  3P GAIN WILD-TYPE   18  419
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                3                18
  YES              36               419
[1] 2 2
[1] FALSE
D5V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    25   2   1   4
  3P GAIN WILD-TYPE 302  10   3  17
D5V12, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              25               302
  R1               2                10
  R2               1                 3
  RX               4                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
  3P GAIN MUTATED                                  0     0
  3P GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           2    29
  3P GAIN WILD-TYPE                        33   338
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                      2                33
  WHITE                                         29               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"
D5V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  25
  3P GAIN WILD-TYPE   5 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   25
  3P GAIN WILD-TYPE    5  320
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              25               320
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    61  14
  3Q GAIN WILD-TYPE 268  73
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               75               341 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               14                73 
$`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-49-AARQ TCGA-50-5072 
         882          287          268          369         6443          246 
TCGA-50-5931 TCGA-50-5941 TCGA-50-5946 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6972 
         267          567          686          280         1178         1475 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7903 TCGA-55-7995 TCGA-55-8085 TCGA-55-8205 
         705           39           19            5           33           33 
TCGA-55-8208 TCGA-55-8614 TCGA-55-A490 TCGA-55-A491 TCGA-64-1677 TCGA-64-1679 
         674          536           48         1952          628         1686 
TCGA-64-5815 TCGA-69-7760 TCGA-69-7978 TCGA-69-7980 TCGA-69-A59K TCGA-73-4676 
         866          202           70          382          214          164 
TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 TCGA-78-7154 TCGA-78-8662 TCGA-86-7711 
         519         1973         1988         1948         1964          630 
TCGA-86-7953 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8358 TCGA-86-8669 
         591           24          479          476           19           34 
TCGA-86-8673 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-95-7043 TCGA-95-7562 
         455          323           60           79            2         1973 
TCGA-95-7947 TCGA-95-8494 TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A8F4 
         477           84          287          116            6          102 
TCGA-MP-A4SV TCGA-MP-A4TF TCGA-S2-AA1A 
        1946         1970          121 

$`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          462          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
         600           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-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1189         1126         1968         1959           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
         864         1559           31          610          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 
         385          174          141          422          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 
         414          165          230          184           89          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-73-4675 TCGA-73-4677 TCGA-73-7498 
         800          467          131           40           38          621 
TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7147 
         305         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          505          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-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
         377          476          830          121          553          605 
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-97-8552 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-A50W TCGA-L9-A743 
         282          238          578          435          266          312 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 
         111          827         1175           84         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 
             6443              2696 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              479               466 
[1] "2.0 - 6443.0 (479.0)" "1.0 - 2696.0 (466.0)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  3Q GAIN MUTATED         2       23       21        12        11         12
  3Q GAIN WILD-TYPE       3       93      111        37        59         56
                   vv
clus                STAGE IIIB STAGE IV
  3Q GAIN MUTATED            0        3
  3Q GAIN WILD-TYPE         11       21
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                23                93
  STAGE IB                21               111
  STAGE IIA               12                37
  STAGE IIB               11                59
  STAGE IIIA              12                56
  STAGE IIIB               0                11
  STAGE IV                 3                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
  3Q GAIN MUTATED    29  46   6   2
  3Q GAIN WILD-TYPE 118 221  36  16
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              29               118
  T2              46               221
  T3               6                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
  3Q GAIN MUTATED    52  19    11
  3Q GAIN WILD-TYPE 249  72    63
D6V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                 52               249
  N1                 19                72
  N2+N3              11                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
  3Q GAIN MUTATED    62   3   0   0  19
  3Q GAIN WILD-TYPE 264  15   1   4 104
D6V6, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               62               264
  M1                3                15
  M1A               0                 1
  M1B               0                 4
  MX               19               104
[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    46  38
  3Q GAIN WILD-TYPE 209 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     46   38
  3Q GAIN WILD-TYPE  209  183
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              46               209
  MALE                38               183
[1] 2 2
[1] FALSE
D6V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3Q GAIN MUTATED                            2
  3Q GAIN WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3Q GAIN MUTATED                                  18
  3Q GAIN WILD-TYPE                                76
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                   58
  3Q GAIN WILD-TYPE                                                245
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3Q GAIN MUTATED                                            1
  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                                             5
                   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)              58
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  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                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               245
  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                      5
  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  80
  3Q GAIN WILD-TYPE  17 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4   80
  3Q GAIN WILD-TYPE   17  375
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                4                17
  YES              80               375
[1] 2 2
[1] FALSE
D6V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    58   2   2   5
  3Q GAIN WILD-TYPE 269  10   2  16
D6V12, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              58               269
  R1               2                10
  R2               2                 2
  RX               5                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
  3Q GAIN MUTATED                                  0     0
  3Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                           6    63
  3Q GAIN WILD-TYPE                        29   304
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                      6                29
  WHITE                                         63               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"
D6V14, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3  59
  3Q GAIN WILD-TYPE   4 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   59
  3Q GAIN WILD-TYPE    4  286
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO              59               286
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    47  19
  4P GAIN WILD-TYPE 282  68
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               66               350 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               19                68 
$`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-49-AARQ TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 
        6443          255         1986          424         1178         1479 
TCGA-55-6712 TCGA-55-7573 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
          24            4          100          600            4           47 
TCGA-55-8302 TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-62-8402 TCGA-62-A471 
          23           48            1           28         1445         1246 
TCGA-64-1676 TCGA-64-1680 TCGA-64-1681 TCGA-69-7980 TCGA-69-8253 TCGA-75-6214 
        1728         1126         1968          382          100         1970 
TCGA-75-7027 TCGA-78-7145 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1956         1973         1963          760         1948         1957 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7539 TCGA-78-7542 
        1950         1937         1965         1972          327         1952 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8278 TCGA-86-8279 TCGA-86-8669 TCGA-86-A456 
         591          508          476          482           34           10 
TCGA-91-6836 TCGA-91-6848 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7937 
         417          224          476           84          605          181 
TCGA-97-8179 TCGA-97-8552 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4TF 
          15          115           84         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          705           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 
         462            6           26           15           33           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
          66          674          216           44           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-A491 TCGA-55-A494 
         106           33           42           29         1952            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-64-5774 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-69-8254 
         165          230          184           70           89           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-73-A9RS TCGA-75-7025 TCGA-75-7031 TCGA-78-7146 
         621          519          305         1967         1965         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 
        1950         1944         1093         1202         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7536 
        1221          678          215         1940         1934         1949 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
        1944          881          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-86-7954 TCGA-86-8054 
          11          630          422         1968         1963          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-86-8280 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-86-8672 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          505          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-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
          34            2         1973          568          377          477 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         830          121          553          964         1965         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        1332          775           22          107          182         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
          87          147          148          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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
           6          266          312          111          102          827 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1175         1946         1951         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1944         1970          142         1955         1971 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                 2 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             6443              2696 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            595.5             458.0 
[1] "1.0 - 6443.0 (595.5)" "2.0 - 2696.0 (458.0)"
[1] "hr=" "1.1"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  4P GAIN MUTATED         4       14       26         6        13          9
  4P GAIN WILD-TYPE       1      102      106        43        57         59
                   vv
clus                STAGE IIIB STAGE IV
  4P GAIN MUTATED            1        7
  4P GAIN WILD-TYPE         10       17
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  4                 1
  STAGE IA                14               102
  STAGE IB                26               106
  STAGE IIA                6                43
  STAGE IIB               13                57
  STAGE IIIA               9                59
  STAGE IIIB               1                10
  STAGE IV                 7                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  53   6   2
  4P GAIN WILD-TYPE 128 214  36  16
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              19               128
  T2              53               214
  T3               6                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
  4P GAIN MUTATED    54  14    11
  4P GAIN WILD-TYPE 247  77    63
D7V5, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0                 54               247
  N1                 14                77
  N2+N3              11                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    53   5   0   2  19
  4P GAIN WILD-TYPE 273  13   1   2 104
D7V6, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               53               273
  M1                5                13
  M1A               0                 1
  M1B               2                 2
  MX               19               104
[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    43  37
  4P GAIN WILD-TYPE 212 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     43   37
  4P GAIN WILD-TYPE  212  184
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              43               212
  MALE                37               184
[1] 2 2
[1] FALSE
D7V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4P GAIN MUTATED                            2
  4P GAIN WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4P GAIN MUTATED                                   9
  4P GAIN WILD-TYPE                                85
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                   62
  4P GAIN WILD-TYPE                                                241
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4P GAIN MUTATED                                            0
  4P GAIN WILD-TYPE                                          5
                   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                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  4P GAIN MUTATED                              0
  4P GAIN WILD-TYPE                            7
D7V9, multiclass
                                                    clus
vv                                                   4P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              62
  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                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               241
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      5
  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  78
  4P GAIN WILD-TYPE  19 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2   78
  4P GAIN WILD-TYPE   19  377
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                2                19
  YES              78               377
[1] 2 2
[1] FALSE
D7V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    54   2   0   3
  4P GAIN WILD-TYPE 273  10   4  18
D7V12, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              54               273
  R1               2                10
  R2               0                 4
  RX               3                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
  4P GAIN MUTATED                                  0     2
  4P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           5    65
  4P GAIN WILD-TYPE                        30   302
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                      5                30
  WHITE                                         65               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"
D7V14, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     2  52
  4P GAIN WILD-TYPE   5 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2   52
  4P GAIN WILD-TYPE    5  293
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              52               293
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    28   6
  4Q GAIN WILD-TYPE 301  81
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               34               382 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6                81 
$`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          600           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-95-8494 TCGA-97-8552 TCGA-MN-A4N5 TCGA-MP-A4T4 
          84          115           84         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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        6443         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-50-7109 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-55-1596 TCGA-55-5899 TCGA-55-6543 
         701         1178         1479         1375           87            2 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
         993         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          705           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-55-8094 TCGA-55-8097 TCGA-55-8205 
         462            6           26            4           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          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-55-8616 TCGA-55-8619 TCGA-55-8620 
           3          146          202           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-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
           1            5           47          162         1216         1289 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 
        1970         2696         2067         2199          910          628 
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-64-5779 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-69-7760 
         427          385          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-69-8254 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-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
          40          164           38          621          519          305 
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-78-7148 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-78-7166 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-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         327          881          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-86-7954 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-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         489          482           16         1955           19           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          35           45           34           18           15          455 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
         405           30           14           39          323         1940 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
          60          310           79          372          842           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          505          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
         297          127          186           34            2         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
         568          377          477          830          121          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         605          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-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
         147           15          148          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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
           6          266          312          111          102          827 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T8 
        1175         1946         1967         1951         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 TCGA-S2-AA1A 
        1955         1971         1490          121 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10                 1 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1956              6443 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            563.5             464.0 
[1] "10.0 - 1956.0 (563.5)" "1.0 - 6443.0 (464.0)" 
[1] "hr=" "1.4"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  4Q GAIN MUTATED         2        5       18         2        10          6
  4Q GAIN WILD-TYPE       3      111      114        47        60         62
                   vv
clus                STAGE IIIB STAGE IV
  4Q GAIN MUTATED            0        2
  4Q GAIN WILD-TYPE         11       22
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 5               111
  STAGE IB                18               114
  STAGE IIA                2                47
  STAGE IIB               10                60
  STAGE IIIA               6                62
  STAGE IIIB               0                11
  STAGE IV                 2                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
  4Q GAIN MUTATED    10  30   5   0
  4Q GAIN WILD-TYPE 137 237  37  18
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1              10               137
  T2              30               237
  T3               5                37
  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  10     7
  4Q GAIN WILD-TYPE 273  81    67
D8V5, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0                 28               273
  N1                 10                81
  N2+N3               7                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
  4Q GAIN MUTATED    32   2   0   0  11
  4Q GAIN WILD-TYPE 294  16   1   4 112
D8V6, multiclass
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               32               294
  M1                2                16
  M1A               0                 1
  M1B               0                 4
  MX               11               112
[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  23
  4Q GAIN WILD-TYPE 233 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     22   23
  4Q GAIN WILD-TYPE  233  198
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              22               233
  MALE                23               198
[1] 2 2
[1] FALSE
D8V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4Q GAIN MUTATED                            0
  4Q GAIN WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4Q GAIN MUTATED                                   4
  4Q GAIN WILD-TYPE                                90
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                   37
  4Q GAIN WILD-TYPE                                                266
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4Q GAIN MUTATED                                            0
  4Q GAIN WILD-TYPE                                          5
                   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                                             4
                   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)              37
  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                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               266
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                                       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  44
  4Q GAIN WILD-TYPE  20 411
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   44
  4Q GAIN WILD-TYPE   20  411
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1                20
  YES              44               411
[1] 2 2
[1] FALSE
D8V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    31   0   0   2
  4Q GAIN WILD-TYPE 296  12   4  19
D8V12, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              31               296
  R1               0                12
  R2               0                 4
  RX               2                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
  4Q GAIN MUTATED                                  0     1
  4Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           2    35
  4Q GAIN WILD-TYPE                        33   332
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                33
  WHITE                                         35               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"
D8V14, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  31
  4Q GAIN WILD-TYPE   6 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   31
  4Q GAIN WILD-TYPE    6  314
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              31               314
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   180  46
  5P GAIN WILD-TYPE 149  41
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              226               190 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               46                41 
$`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-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 
         444          592          557         1970          882          719 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47F TCGA-44-A4SS TCGA-49-4501 
         385           99          466          337          415         1421 
TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
         428          896          157         1700          369          890 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 
         354         2174         2146          455          944         1499 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 TCGA-50-6597 
         282         2370          653          567          686         1015 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
         255         1986         1971          424          701         1178 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
        1479           87            2         1475           67         1826 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 
        1233         1170            6            4           95          705 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
          39           39           34           19          197           21 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
         600            4           47           46           66          674 
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-95-7947 
         218          297          127          186           34          477 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 
         476          830           84          964         1965         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8547 TCGA-97-8552 
         775          181          182         1965          148          115 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE 
         271          427          170          154          287          282 
TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SW 
         578            6          312          111           84         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        1951         1954         1954         1957         1951         1944 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-S2-AA1A 
        1970          142         1971          121 

$`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-44-7662 
         302          704         1938         1978          366          218 
TCGA-44-7671 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU 
         535          260          486          287          351           76 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-6742 TCGA-49-6745 
        1932         1081          999          268          445          522 
TCGA-49-AARQ TCGA-50-5055 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5942 
        6443          785          246          267         1091          883 
TCGA-50-5944 TCGA-50-8460 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 
         764          105          280         1375          993           24 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1239           25         2151           18           35          121 
TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7914 TCGA-55-7994 
          40           24           54           16            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 
           5           33          462          100            6           26 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8299 TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 
          15           33          216           29            3          146 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A492 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46V 
          49          106            1         1289         1970         2199 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1681 TCGA-64-5775 
         910         1728          628         1189         1968           62 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 
         864          866          610          573          385          186 
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-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4677 TCGA-73-7498 
         214          711          912          800           38          621 
TCGA-73-A9RS TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
         305         1967         1956         1973         1988         1944 
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-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
        1940         1937         1944          881         1952         1971 
TCGA-78-8660 TCGA-80-5607 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 
        1954         1965           11          422         1968         1963 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 
         508         1963           24          489          476         1955 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
          45           34           18          405           10           14 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 
          39         1940          310           79          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-95-7043 TCGA-95-7562 
          35          492          505          174            2         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 
         568          377          121          553          605         1932 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M2 
          22          107           87          147           15          197 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 
         392          459           44          114          238          435 
TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV 
         116          266          102          827         1175         1946 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TI TCGA-MP-A5C7 
        1980         1970         1955         1490 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                 1 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             2696              6443 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            476.5             469.0 
[1] "2.0 - 2696.0 (476.5)" "1.0 - 6443.0 (469.0)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  5P GAIN MUTATED         3       63       75        32        30         34
  5P GAIN WILD-TYPE       2       53       57        17        40         34
                   vv
clus                STAGE IIIB STAGE IV
  5P GAIN MUTATED            8       13
  5P GAIN WILD-TYPE          3       11
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                63                53
  STAGE IB                75                57
  STAGE IIA               32                17
  STAGE IIB               30                40
  STAGE IIIA              34                34
  STAGE IIIB               8                 3
  STAGE IV                13                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    85 148  16   8
  5P GAIN WILD-TYPE  62 119  26  10
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              85                62
  T2             148               119
  T3              16                26
  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   161  48    42
  5P GAIN WILD-TYPE 140  43    32
D9V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                161               140
  N1                 48                43
  N2+N3              42                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  5P GAIN MUTATED   171   9   0   3  72
  5P GAIN WILD-TYPE 155   9   1   1  51
D9V6, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              171               155
  M1                9                 9
  M1A               0                 1
  M1B               3                 1
  MX               72                51
[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   148 110
  5P GAIN WILD-TYPE 107 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    148  110
  5P GAIN WILD-TYPE  107  111
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE             148               107
  MALE               110               111
[1] 2 2
[1] FALSE
D9V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5P GAIN MUTATED                            7
  5P GAIN WILD-TYPE                          8
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5P GAIN MUTATED                                  45
  5P GAIN WILD-TYPE                                49
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                  176
  5P GAIN WILD-TYPE                                                127
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5P GAIN MUTATED                                            2
  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                                             3
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  5P GAIN MUTATED                              2
  5P GAIN WILD-TYPE                            5
D9V9, multiclass
                                                    clus
vv                                                   5P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             176
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       2
  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                                         8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               127
  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                      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"
D9V10, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    14 244
  5P GAIN WILD-TYPE   7 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     14  244
  5P GAIN WILD-TYPE    7  211
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               14                 7
  YES             244               211
[1] 2 2
[1] FALSE
D9V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED   182   6   1  11
  5P GAIN WILD-TYPE 145   6   3  10
D9V12, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0             182               145
  R1               6                 6
  R2               1                 3
  RX              11                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
  5P GAIN MUTATED                                  1     3
  5P GAIN WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          18   205
  5P GAIN WILD-TYPE                        17   162
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                     18                17
  WHITE                                        205               162
[1] 4 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     4 193
  5P GAIN WILD-TYPE   3 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4  193
  5P GAIN WILD-TYPE    3  152
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             193               152
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    79  23
  5Q GAIN WILD-TYPE 250  64
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              102               314 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               23                64 
$`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          705          197           21          600           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-A48Z 
          66          674           15          202          536           29 
TCGA-55-A493 TCGA-55-A4DG TCGA-62-A46U TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 
          28          162         2067         1126           62         1559 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-8253 
         174          141          422          202          690          100 
TCGA-73-4670 TCGA-73-4675 TCGA-75-6214 TCGA-78-7147 TCGA-78-7153 TCGA-78-7154 
         131           40         1970         1950          760         1948 
TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 
        1950         1965         1972         1949          327          994 
TCGA-80-5608 TCGA-83-5908 TCGA-86-7711 TCGA-86-8055 TCGA-86-8280 TCGA-86-8358 
        1972          824          630           10           16           19 
TCGA-86-8359 TCGA-86-A4D0 TCGA-91-6836 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
          26           30          417          218          297          127 
TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-8172 
         477          830           84          964         1965          182 
TCGA-97-8174 TCGA-97-8552 TCGA-97-A4M7 TCGA-J2-A4AE TCGA-MP-A4T2 TCGA-MP-A4T4 
        1965          115          271          282         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-S2-AA1A 
        1954         1957         1970          142         1971          121 

$`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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        6443         2174         2146          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 
         246          282          267         1091         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-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
         280          701         1178         1375           87          993 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
          24         1239           25         1233         2151         1170 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7576 TCGA-55-7725 
          18           35          121            6           40           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-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
           3           31            5           33          462          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-55-8505 TCGA-55-8506 TCGA-55-8507 
         216           44           23           29           11            8 
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-A48X TCGA-55-A48Y TCGA-55-A490 
          49           66          106           33           42           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 
        1952            1            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-64-1681 TCGA-64-5774 
        1728          628         1189         1686         1968         1959 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        1305          864          866           31          610          573 
TCGA-67-3773 TCGA-67-3774 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
         427          385          186          414          165          230 
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-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
         467          164           38          621          519          305 
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-78-7155 TCGA-78-7156 TCGA-78-7158 
        1093         1963         1202         1957         1961         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
        1221          678          215         1940         1934         1937 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
        1944          881         1952         1949         1971         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 
        1954         1964         1965         1959           11          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-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
          13           24          479          489          476          482 
TCGA-86-8281 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
        1955           35           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-91-6831 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          505          174           36 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
          44          186           34            2         1973          568 
TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 
         377          476          121          553          605         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
        1332          775          181           22          107           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 
         147           15          148          197          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-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
         238          578          435          116            6          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         312          111          102          827         1175           84 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1946         1967         1980         1951         1944         1970 
TCGA-MP-A4TI TCGA-MP-A5C7 
        1955         1490 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                 1 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2067              6443 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            460.5             477.5 
[1] "2.0 - 2067.0 (460.5)" "1.0 - 6443.0 (477.5)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  5Q GAIN MUTATED         1       29       33        13        14         18
  5Q GAIN WILD-TYPE       4       87       99        36        56         50
                   vv
clus                STAGE IIIB STAGE IV
  5Q GAIN MUTATED            3        6
  5Q GAIN WILD-TYPE          8       18
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                29                87
  STAGE IB                33                99
  STAGE IIA               13                36
  STAGE IIB               14                56
  STAGE IIIA              18                50
  STAGE IIIB               3                 8
  STAGE IV                 6                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
  5Q GAIN MUTATED    37  71   6   3
  5Q GAIN WILD-TYPE 110 196  36  15
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              37               110
  T2              71               196
  T3               6                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
  5Q GAIN MUTATED    73  20    20
  5Q GAIN WILD-TYPE 228  71    54
D10V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                 73               228
  N1                 20                71
  N2+N3              20                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
  5Q GAIN MUTATED    80   6   0   0  29
  5Q GAIN WILD-TYPE 246  12   1   4  94
D10V6, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               80               246
  M1                6                12
  M1A               0                 1
  M1B               0                 4
  MX               29                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"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    73  44
  5Q GAIN WILD-TYPE 182 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     73   44
  5Q GAIN WILD-TYPE  182  177
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              73               182
  MALE                44               177
[1] 2 2
[1] FALSE
D10V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5Q GAIN MUTATED                            5
  5Q GAIN WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5Q GAIN MUTATED                                  18
  5Q GAIN WILD-TYPE                                76
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                   79
  5Q GAIN WILD-TYPE                                                224
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5Q GAIN MUTATED                                            2
  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                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  5Q GAIN MUTATED                              2
  5Q GAIN WILD-TYPE                            5
D10V9, multiclass
                                                    clus
vv                                                   5Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              79
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       2
  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                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               224
  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                      5
  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     8 109
  5Q GAIN WILD-TYPE  13 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      8  109
  5Q GAIN WILD-TYPE   13  346
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                8                13
  YES             109               346
[1] 2 2
[1] FALSE
D10V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    81   3   1   5
  5Q GAIN WILD-TYPE 246   9   3  16
D10V12, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              81               246
  R1               3                 9
  R2               1                 3
  RX               5                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
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           6    97
  5Q GAIN WILD-TYPE                        29   270
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                      6                29
  WHITE                                         97               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"
D10V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  86
  5Q GAIN WILD-TYPE   6 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   86
  5Q GAIN WILD-TYPE    6  259
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              86               259
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    96  20
  6P GAIN WILD-TYPE 233  67
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              116               300 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               20                67 
$`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-55-8208 TCGA-55-8507 
          33           15           33           46          674            8 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 
           9            3          202          536           15           66 
TCGA-55-A48Y TCGA-55-A490 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46V TCGA-62-A471 
          42           48         1970         2696         2199         1246 
TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-67-3771 TCGA-67-3773 
         628         1126         1959          864          610          427 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-69-8255 TCGA-71-6725 
         690          414          165           89          129           61 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         912          467          131           38          621          519 
TCGA-75-6214 TCGA-78-7147 TCGA-78-7149 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 
        1970         1950         1093         1957         1221          215 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 
        1940         1937         1965          327         1952          994 
TCGA-78-8655 TCGA-78-8662 TCGA-86-6851 TCGA-86-7954 TCGA-86-8074 TCGA-86-8075 
        1981         1964         1959         1963           24          479 
TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8674 TCGA-91-6835 TCGA-91-6847 
         482         1955           19          405           79          842 
TCGA-91-6848 TCGA-91-8499 TCGA-95-7562 TCGA-95-7944 TCGA-97-7546 TCGA-97-7553 
         224           36         1973          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-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 
         114          282            6          111         1175           84 
TCGA-MP-A4SV TCGA-MP-A4TE 
        1946         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-49-AARQ 
         157         1700          369          890          522         6443 
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-50-5935 TCGA-50-5942 TCGA-50-6597 
         246          282         1091          653          883         1015 
TCGA-50-8460 TCGA-53-7626 TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 
         105         1971         1178           87            2           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-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
          95           40          705           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          24           54           16          197           21            3 
TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          31          462          100            6          600           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
           4           47           66          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8513 TCGA-55-8616 
          29           11           15          228          146           48 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
          49          106           33           29         1952            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
          28            5           47          162         1216         1289 
TCGA-62-8402 TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
        1445         2067          910         1728         1189         1686 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        1968           62         1305         1559          866           31 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
         573          385          174          141          422          202 
TCGA-69-7761 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
         186          230          184           70          382          100 
TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 
          77          214         1600          711          800           40 
TCGA-73-4676 TCGA-73-A9RS TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         164          305         1967         1956         1965         1973 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1988         1944         1963         1202          760         1948 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 
        1961         1963          678         1950         1934         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 
        1949         1944          881         1949         1971         1954 
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-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
        1968          591          508          745           10         1963 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
          13          489          476           16           26           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 
          45           34           18           15          455           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-91-6836 TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         310          417          372           35          492          505 
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-95-8039 
          34            2          568          477          476          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
          84          121          553          605         1965         1932 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
         775          181           22          182         1965           87 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
         148          115          197          392          459           44 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         154          287          238          578          435          116 
TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4T2 
         266          312          102          827         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-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970          142         1955         1971         1490          121 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                 1 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             2696              6443 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            546.5             458.0 
[1] "3.0 - 2696.0 (546.5)" "1.0 - 6443.0 (458.0)"
[1] "hr=" "1.5"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  6P GAIN MUTATED         1       41       33        12        14         17
  6P GAIN WILD-TYPE       4       75       99        37        56         51
                   vv
clus                STAGE IIIB STAGE IV
  6P GAIN MUTATED            4       10
  6P GAIN WILD-TYPE          7       14
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                41                75
  STAGE IB                33                99
  STAGE IIA               12                37
  STAGE IIB               14                56
  STAGE IIIA              17                51
  STAGE IIIB               4                 7
  STAGE IV                10                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
  6P GAIN MUTATED    48  70   8   5
  6P GAIN WILD-TYPE  99 197  34  13
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              48                99
  T2              70               197
  T3               8                34
  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  19    21
  6P GAIN WILD-TYPE 213  72    53
D11V5, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0                 88               213
  N1                 19                72
  N2+N3              21                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 GAIN MUTATED    91   6   1   2  32
  6P GAIN WILD-TYPE 235  12   0   2  91
D11V6, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               91               235
  M1                6                12
  M1A               1                 0
  M1B               2                 2
  MX               32                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"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    69  63
  6P GAIN WILD-TYPE 186 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     69   63
  6P GAIN WILD-TYPE  186  158
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              69               186
  MALE                63               158
[1] 2 2
[1] FALSE
D11V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6P GAIN MUTATED                            7
  6P GAIN WILD-TYPE                          8
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6P GAIN MUTATED                                  26
  6P GAIN WILD-TYPE                                68
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                   82
  6P GAIN WILD-TYPE                                                221
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6P GAIN MUTATED                                            0
  6P GAIN WILD-TYPE                                          5
                   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                                             4
                   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                               26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              82
  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                                         8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               221
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      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"
D11V10, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5 127
  6P GAIN WILD-TYPE  16 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5  127
  6P GAIN WILD-TYPE   16  328
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                5                16
  YES             127               328
[1] 2 2
[1] FALSE
D11V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    94   2   0   6
  6P GAIN WILD-TYPE 233  10   4  15
D11V12, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              94               233
  R1               2                10
  R2               0                 4
  RX               6                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 GAIN MUTATED                                  1     4
  6P GAIN WILD-TYPE                                0     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           7   109
  6P GAIN WILD-TYPE                        28   258
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                      7                28
  WHITE                                        109               258
[1] 4 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  98
  6P GAIN WILD-TYPE   3 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4   98
  6P GAIN WILD-TYPE    3  247
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO              98               247
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    42   6
  6Q GAIN WILD-TYPE 287  81
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               368 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6                81 
$`6Q GAIN MUTATED`
TCGA-05-4249 TCGA-05-4420 TCGA-05-4432 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
        1523          912          761          264         1952         1492 
TCGA-44-7667 TCGA-44-7670 TCGA-49-6742 TCGA-50-6597 TCGA-50-7109 TCGA-53-A4EZ 
         557          882          445         1015          255          280 
TCGA-55-1596 TCGA-55-7910 TCGA-55-7995 TCGA-55-8097 TCGA-55-8206 TCGA-55-8507 
        1375          197            5           15           46            8 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8620 TCGA-62-A471 TCGA-67-3773 TCGA-69-7763 
           9          202           66         1246          427          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-71-6725 TCGA-73-4677 TCGA-78-7167 
         414          165           89           61           38         1937 
TCGA-78-7220 TCGA-78-7539 TCGA-78-8662 TCGA-86-6851 TCGA-86-7954 TCGA-86-8074 
        1965          327         1964         1959         1963           24 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-95-7562 TCGA-95-7944 TCGA-97-7546 
         842          224           36         1973          377          964 
TCGA-97-8177 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AE TCGA-L9-A7SV TCGA-MN-A4N4 
         147          427          170          282          111         1175 

$`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-05-5425 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-38-4626 TCGA-38-4627 TCGA-38-4629 
          14          225          182         1962         1147          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-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
         366          218         1970          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-49-4501 
         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-49-AARQ TCGA-50-5045 
         369          890          522          354         6443         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-50-8460 TCGA-53-7624 TCGA-53-7626 
         883          764          686          105         1986         1971 
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-55-6971 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          705 
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-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
          16           21            3           31           33          462 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
         100            6          600           26            4           47 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           66          674          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
          29           11           15          228            3          146 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
         536           15           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-62-8399 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-67-3770 
          62         1305          864         1559          866           31 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
         610          573          385          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
         202          186          230          184           70          382 
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-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         912          800          467          131           40          164 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
         621          519          305         1970         1967         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        1965         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-78-7159 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-78-7540 TCGA-78-7542 
        1934         1972         1949         1944          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-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1972          824           11          630          422         1968 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
         591          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-86-8358 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-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         417          372           35          492          505          174 
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-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
           2          568          477          476          830           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         121          553          605         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-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
          87           15          148          115          197          271 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         392          459           44          154          114          287 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
         238          578          435          116            6          266 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         312          102          827           84         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 TCGA-S2-AA1A 
        1490          121 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                 1 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             1973              6443 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            395.5             484.0 
[1] "5.0 - 1973.0 (395.5)" "1.0 - 6443.0 (484.0)"
[1] "hr=" "1.2"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  6Q GAIN MUTATED         1       13       15         8         7          6
  6Q GAIN WILD-TYPE       4      103      117        41        63         62
                   vv
clus                STAGE IIIB STAGE IV
  6Q GAIN MUTATED            1        5
  6Q GAIN WILD-TYPE         10       19
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                13               103
  STAGE IB                15               117
  STAGE IIA                8                41
  STAGE IIB                7                63
  STAGE IIIA               6                62
  STAGE IIIB               1                10
  STAGE IV                 5                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
  6Q GAIN MUTATED    17  32   4   2
  6Q GAIN WILD-TYPE 130 235  38  16
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              17               130
  T2              32               235
  T3               4                38
  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    36  12     7
  6Q GAIN WILD-TYPE 265  79    67
D12V5, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0                 36               265
  N1                 12                79
  N2+N3               7                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
  6Q GAIN MUTATED    37   3   0   1  15
  6Q GAIN WILD-TYPE 289  15   1   3 108
D12V6, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               37               289
  M1                3                15
  M1A               0                 1
  M1B               1                 3
  MX               15               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"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    31  25
  6Q GAIN WILD-TYPE 224 196
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     31   25
  6Q GAIN WILD-TYPE  224  196
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              31               224
  MALE                25               196
[1] 2 2
[1] FALSE
D12V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6Q GAIN MUTATED                            3
  6Q GAIN WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6Q GAIN MUTATED                                  11
  6Q GAIN WILD-TYPE                                83
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                   38
  6Q GAIN WILD-TYPE                                                265
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6Q GAIN MUTATED                                            0
  6Q GAIN WILD-TYPE                                          5
                   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                                             5
                   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                               11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              38
  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                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               265
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      5
  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  20 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   55
  6Q GAIN WILD-TYPE   20  400
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                1                20
  YES              55               400
[1] 2 2
[1] FALSE
D12V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    38   0   0   4
  6Q GAIN WILD-TYPE 289  12   4  17
D12V12, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              38               289
  R1               0                12
  R2               0                 4
  RX               4                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
  6Q GAIN MUTATED                                  0     2
  6Q GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           6    43
  6Q GAIN WILD-TYPE                        29   324
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                      6                29
  WHITE                                         43               324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  43
  6Q GAIN WILD-TYPE   5 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   43
  6Q GAIN WILD-TYPE    5  302
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              43               302
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   171  41
  7P GAIN WILD-TYPE 158  46
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              212               204 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               41                46 
$`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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
        6443         2174         2146          785          944          246 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 
        2370          567          764          686         1015         1986 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 
        1375           87            2           24           25         1475 
TCGA-55-6980 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 
          67         1233         1170           35          121           40 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 
         705           39           34           16          197           31 
TCGA-55-8085 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 
          33          600           26           47           33           46 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 
          44           23           29          228            9          202 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
          15           48           66           29           48         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8397 TCGA-62-8398 
           1           28            5          162         1289         1970 
TCGA-62-8399 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        2696          910         1728         1686         1126         1968 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 
         864         1559          610          573          422          202 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K 
         414          165          184           89          129          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
          61         1600          912          467          131           40 
TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 
         164          519          305         1970         1967         1973 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 
        1950         1963         1948         1957          678          215 
TCGA-78-7163 TCGA-78-7535 TCGA-78-7540 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 
        1950         1972          881         1952         1981         1964 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 
         824           11          422          591          508           10 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
          13           24          479          482           16           19 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 
          26           45           15          455           10           14 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-A4BC 
         310           79          842          224          505           44 
TCGA-93-7348 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 
         127         1973          568          377          477           84 
TCGA-95-A4VN TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 
         553         1332          775          181          107           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8025 
         147           15          148          115          271          427 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
         170          154          114          287          282          578 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 
         116            6          266          111          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
          84         1951         1957         1980         1951         1944 
TCGA-MP-A4TK TCGA-S2-AA1A 
        1971          121 

$`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          462          100            6            4           15 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          66          674          216           11            8           15 
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-A4DF TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
          42           47         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-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
         866           31          427          385          174          141 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
         186          690          230           70          382          100 
TCGA-69-8254 TCGA-73-4659 TCGA-73-4666 TCGA-73-4677 TCGA-73-7498 TCGA-75-7027 
          77          711          800           38          621         1956 
TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
        1965         1988         1944         1093         1202          760 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
        1961         1963         1221         1940         1934         1937 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 
        1965         1949         1944          327          994         1949 
TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 
        1971         1954         1965         1972         1959          630 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 
        1968         1963          745         1963          489          476 
TCGA-86-8281 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A4D0 
        1955           35           34           18          405           30 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 
          39          323         1940           60          417          372 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
          35          492          174           36          218          297 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
         186           34            2          476          830          121 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 TCGA-97-8172 
         605          964         1965         1932           22          182 
TCGA-97-8174 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-A4AG 
        1965          197          392          459           44          238 
TCGA-L4-A4E6 TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
         435          312          102         1946         1967         1954 
TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1954         1970         1970          142         1955         1490 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                1                 2 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             6443              2199 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            455.0             490.5 
[1] "1.0 - 6443.0 (455.0)" "2.0 - 2199.0 (490.5)"
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  7P GAIN MUTATED         3       53       70        25        35         43
  7P GAIN WILD-TYPE       2       63       62        24        35         25
                   vv
clus                STAGE IIIB STAGE IV
  7P GAIN MUTATED            6       15
  7P GAIN WILD-TYPE          5        9
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                53                63
  STAGE IB                70                62
  STAGE IIA               25                24
  STAGE IIB               35                35
  STAGE IIIA              43                25
  STAGE IIIB               6                 5
  STAGE IV                15                 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    70 144  27   8
  7P GAIN WILD-TYPE  77 123  15  10
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              70                77
  T2             144               123
  T3              27                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   145  46    52
  7P GAIN WILD-TYPE 156  45    22
D13V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                145               156
  N1                 46                45
  N2+N3              52                22
[1] 3 2
[1] 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   167  11   1   2  66
  7P GAIN WILD-TYPE 159   7   0   2  57
D13V6, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              167               159
  M1               11                 7
  M1A               1                 0
  M1B               2                 2
  MX               66                57
[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   135 115
  7P GAIN WILD-TYPE 120 106
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    135  115
  7P GAIN WILD-TYPE  120  106
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             135               120
  MALE               115               106
[1] 2 2
[1] FALSE
D13V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7P GAIN MUTATED                            5
  7P GAIN WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7P GAIN MUTATED                                  43
  7P GAIN WILD-TYPE                                51
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                  172
  7P GAIN WILD-TYPE                                                131
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7P GAIN MUTATED                                            4
  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                                               4
  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                               43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             172
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  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                    4
  MUCINOUS (COLLOID) CARCINOMA                                     1
                                                    clus
vv                                                   7P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               131
  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     9 241
  7P GAIN WILD-TYPE  12 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9  241
  7P GAIN WILD-TYPE   12  214
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                9                12
  YES             241               214
[1] 2 2
[1] FALSE
D13V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   168   6   3  12
  7P GAIN WILD-TYPE 159   6   1   9
D13V12, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             168               159
  R1               6                 6
  R2               3                 1
  RX              12                 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
  7P GAIN MUTATED                                  1     4
  7P GAIN WILD-TYPE                                0     2
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          23   190
  7P GAIN WILD-TYPE                        12   177
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                     23                12
  WHITE                                        190               177
[1] 4 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     3 186
  7P GAIN WILD-TYPE   4 159
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3  186
  7P GAIN WILD-TYPE    4  159
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             186               159
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   142  36
  7Q GAIN WILD-TYPE 187  51
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              178               238 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               36                51 
$`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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 
         157          522         6443         2174         2146          944 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
         246          282          653          567          764          686 
TCGA-50-6597 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1596 TCGA-55-6543 
        1015         1986          280          701         1375            2 
TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 TCGA-55-6987 
          24           25         1475           67         1233         1170 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 
          35          121           40          705           39           16 
TCGA-55-7910 TCGA-55-7994 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 
         197           31          600           26           47           33 
TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 
          46           44           23           29            8          228 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
           9          202           48           66           29           48 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
           1           28            5         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-67-3772 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        1559          573          202          690          414          165 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
         184           70           89          214           61         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-73-7499 TCGA-78-7145 TCGA-78-7147 TCGA-78-7160 TCGA-78-7163 TCGA-78-7220 
         519         1973         1950          678         1950         1965 
TCGA-78-7540 TCGA-78-8655 TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 
         881         1981          824           11          422          591 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8280 TCGA-86-8359 
         508           10           13          479           16           26 
TCGA-86-8668 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4P7 TCGA-91-6835 TCGA-91-6847 
          45           15          455           14           79          842 
TCGA-91-6848 TCGA-91-8496 TCGA-91-A4BC TCGA-93-7348 TCGA-95-7562 TCGA-95-7567 
         224          505           44          127         1973          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         377          477           84         1332          775          181 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-99-8025 TCGA-99-8033 
         107           87           15          115          427          170 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV 
         154          287          578            6          266          111 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4T9 
         827         1175         1946         1951         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TK TCGA-S2-AA1A 
        1951         1944         1971          121 

$`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 
         462          100            6            4           15           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
         674          216           11           15            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-A491 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8402 TCGA-62-A46U 
        1952           47          162         1216         1445         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 
        2199         1246          628         1189         1959           62 
TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 
        1305          866           31          610          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7973 TCGA-69-7980 
         174          141          422          186          230          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-73-4668 TCGA-73-4677 TCGA-73-7498 
         100           77          129          467           38          621 
TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
         305         1970         1967         1956         1965         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-78-7161 TCGA-78-7162 
        1957         1961         1963         1221          215         1940 
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-78-7542 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-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
        1965         1972         1959          630         1968         1963 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
         745         1963           24          489          476          482 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 
        1955           19           35           34           18          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-91-6836 TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 
         310          417          372           35          492          174 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
          36          218          297          186           34            2 
TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
         476          830          121          553          605          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 
        1965         1932           22          182         1965          147 
TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
         148          197          271          392          459           44 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A743 
         114          282          238          435          116          312 
TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE 
         102           84         1967         1954         1954         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1970          142         1955         1490 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                1                 2 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             6443              2370 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              466               476 
[1] "1.0 - 6443.0 (466.0)" "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         3       46       52        21        27         37
  7Q GAIN WILD-TYPE       2       70       80        28        43         31
                   vv
clus                STAGE IIIB STAGE IV
  7Q GAIN MUTATED            5       14
  7Q GAIN WILD-TYPE          6       10
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                46                70
  STAGE IB                52                80
  STAGE IIA               21                28
  STAGE IIB               27                43
  STAGE IIIA              37                31
  STAGE IIIB               5                 6
  STAGE IV                14                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
  7Q GAIN MUTATED    59 120  18   7
  7Q GAIN WILD-TYPE  88 147  24  11
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              59                88
  T2             120               147
  T3              18                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
  7Q GAIN MUTATED   117  38    43
  7Q GAIN WILD-TYPE 184  53    31
D14V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                117               184
  N1                 38                53
  N2+N3              43                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
  7Q GAIN MUTATED   134  11   1   1  56
  7Q GAIN WILD-TYPE 192   7   0   3  67
D14V6, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              134               192
  M1               11                 7
  M1A               1                 0
  M1B               1                 3
  MX               56                67
[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   108  97
  7Q GAIN WILD-TYPE 147 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    108   97
  7Q GAIN WILD-TYPE  147  124
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             108               147
  MALE                97               124
[1] 2 2
[1] FALSE
D14V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7Q GAIN MUTATED                            6
  7Q GAIN WILD-TYPE                          9
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7Q GAIN MUTATED                                  38
  7Q GAIN WILD-TYPE                                56
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                  139
  7Q GAIN WILD-TYPE                                                164
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7Q GAIN MUTATED                                            4
  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                                             4
                   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                               38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             139
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       4
  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                                         9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               164
  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                      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"
D14V10, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    12 193
  7Q GAIN WILD-TYPE   9 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     12  193
  7Q GAIN WILD-TYPE    9  262
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               12                 9
  YES             193               262
[1] 2 2
[1] FALSE
D14V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   133   4   3  11
  7Q GAIN WILD-TYPE 194   8   1  10
D14V12, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             133               194
  R1               4                 8
  R2               3                 1
  RX              11                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
  7Q GAIN MUTATED                                  0     3
  7Q GAIN WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          19   161
  7Q GAIN WILD-TYPE                        16   206
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                     19                16
  WHITE                                        161               206
[1] 4 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     2 159
  7Q GAIN WILD-TYPE   5 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  159
  7Q GAIN WILD-TYPE    5  186
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             159               186
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    81  21
  8P GAIN WILD-TYPE 248  66
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              102               314 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               21                66 
$`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          705 
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-71-6725 TCGA-73-4658 TCGA-73-4659 
         414          230          184           61         1600          711 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-7027 TCGA-75-7031 
         131           40          164           38         1956         1965 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7158 TCGA-78-7159 TCGA-78-7535 
        1944         1093          760         1963         1221         1972 
TCGA-80-5607 TCGA-86-7701 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
        1965           11           16           26           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-95-A4VP TCGA-97-7547 TCGA-97-7553 TCGA-97-8172 
         568          476          605         1965         1332          182 
TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8025 TCGA-99-8033 TCGA-L9-A444 TCGA-L9-A743 
         115          197          427          170            6          312 
TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1951         1957         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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
         522          354         6443         2174         2146          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
         944         1499          282          267         1091          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         567          883         1015          105         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
         424          280         1178         1479           87            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
         993           24           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-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
          40           39           39           34           24           54 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          19          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33          462          100            6          600           26 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
           4           15           33           66          674          216 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          23           29           11           15          228            9 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
           3          146          202           48           49          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF 
          33           42         1952            1           28           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U 
         162         1216         1289         2696         1445         2067 
TCGA-62-A46V TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
        2199         1728         1189         1686         1968         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
          62         1305         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-69-7761 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         202          186          165           70           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4662 TCGA-73-4666 
         100           77          129          214          912          800 
TCGA-73-4668 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 
         467          621          519          305         1970         1967 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
        1973         1988         1950         1963         1202         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1957         1961          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-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 
        1954         1964         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-86-8668 TCGA-86-8671 
         476          482         1955           19           45           18 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
          15          455           10           30           14           39 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
        1940           60           79          417          842          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
          35          505          174           36           44          218 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 
         127          186           34            2         1973          377 
TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 
         477          830           84          121          553          964 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
        1932          775          181           22          107         1965 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M7 TCGA-99-7458 
          87          147           15          148          271          392 
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-A50W TCGA-L9-A7SV 
         238          578          435          116          266          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         102          827         1175           84         1946         1967 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TK 
        1954         1954         1980         1944         1955         1971 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                 1 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             2370              6443 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            484.0             471.5 
[1] "5.0 - 2370.0 (484.0)" "1.0 - 6443.0 (471.5)"
[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        11        16         19
  8P GAIN WILD-TYPE       3       94       95        38        54         49
                   vv
clus                STAGE IIIB STAGE IV
  8P GAIN MUTATED            4        6
  8P GAIN WILD-TYPE          7       18
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                22                94
  STAGE IB                37                95
  STAGE IIA               11                38
  STAGE IIB               16                54
  STAGE IIIA              19                49
  STAGE IIIB               4                 7
  STAGE IV                 6                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
  8P GAIN MUTATED    26  75  12   3
  8P GAIN WILD-TYPE 121 192  30  15
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              26               121
  T2              75               192
  T3              12                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
  8P GAIN MUTATED    73  20    21
  8P GAIN WILD-TYPE 228  71    53
D15V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                 73               228
  N1                 20                71
  N2+N3              21                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    81   5   0   1  29
  8P GAIN WILD-TYPE 245  13   1   3  94
D15V6, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               81               245
  M1                5                13
  M1A               0                 1
  M1B               1                 3
  MX               29                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"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    49  68
  8P GAIN WILD-TYPE 206 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     49   68
  8P GAIN WILD-TYPE  206  153
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              49               206
  MALE                68               153
[1] 2 2
[1] FALSE
D15V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8P GAIN MUTATED                            5
  8P GAIN WILD-TYPE                         10
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8P GAIN MUTATED                                  26
  8P GAIN WILD-TYPE                                68
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                   74
  8P GAIN WILD-TYPE                                                229
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8P GAIN MUTATED                                            0
  8P GAIN WILD-TYPE                                          5
                   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                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  8P GAIN MUTATED                              1
  8P GAIN WILD-TYPE                            6
D15V9, multiclass
                                                    clus
vv                                                   8P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              74
  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                                        10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               229
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      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"
D15V10, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     7 110
  8P GAIN WILD-TYPE  14 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      7  110
  8P GAIN WILD-TYPE   14  345
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                7                14
  YES             110               345
[1] 2 2
[1] FALSE
D15V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    77   6   1   3
  8P GAIN WILD-TYPE 250   6   3  18
D15V12, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              77               250
  R1               6                 6
  R2               1                 3
  RX               3                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
  8P GAIN MUTATED                                  0     2
  8P GAIN WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           7    94
  8P GAIN WILD-TYPE                        28   273
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                28
  WHITE                                         94               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"
D15V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0  89
  8P GAIN WILD-TYPE   7 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   89
  8P GAIN WILD-TYPE    7  256
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              89               256
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   153  43
  8Q GAIN WILD-TYPE 176  44
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              196               220 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               43                44 
$`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          705           16            3           31           33 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 
          26           47           15           33           46           44 
TCGA-55-8302 TCGA-55-8507 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
          23            8            9          202          536           15 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
          48           66           42           29           48         1952 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 
          28            5          162         1216         1970         1445 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 
        1246          910          628         1189         1126           62 
TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 
         864           31          610          202          690          414 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
         230          184           89          129          214           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
        1600          711          131           40          164           38 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 
         519         1970         1956         1965         1988         1944 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7220 
        1093         1202         1963         1221          215         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8660 TCGA-78-8662 
        1972         1949          327         1952         1954         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-86-7701 TCGA-86-7954 TCGA-86-8054 TCGA-86-8280 
        1965         1972           11         1963          745           16 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
          26           35           34           15          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 
          30           14          323          310          417          372 
TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-93-7347 TCGA-93-8067 TCGA-95-7043 
         842          492           36          297          186            2 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
        1973          568          476          553          605         1965 
TCGA-97-7553 TCGA-97-8172 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8025 
        1332          182           15          115          197          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-L9-A443 
         459           44          170          114          287          116 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
           6          266          312          102         1175           84 
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-49-AARQ 
        1700          445          369          890          522         6443 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 
        2174         2146          785         1499          282         1091 
TCGA-50-5935 TCGA-50-5942 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         653          883         1015          105         1986         1971 
TCGA-55-1594 TCGA-55-6543 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 
        1178            2           67         1826         2151         1170 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 
          18          121            6            4           40           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
          39           34           24           54           19          197 
TCGA-55-7911 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
          21            5          462          100            6          600 
TCGA-55-8094 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 
           4           66          674          216           29           11 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 
          15          228            3          146           49          106 
TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U 
          33            1           47         1289         2696         2067 
TCGA-62-A46V TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
        2199         1728         1686         1968         1959         1305 
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-67-6217 TCGA-69-7761 TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 
         141          422          186          165           70          382 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-7498 
         100           77          912          800          467          621 
TCGA-73-A9RS TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7153 
         305         1967         1973         1950         1963          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
        1948         1957         1961          678         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 
        1934         1937         1944          881          994         1949 
TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
        1971         1981          824         1959          630          422 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
        1968          591          508           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-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-A4P8 TCGA-91-6829 
          19           45           18          455           39         1940 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
          60           79          224           35          505          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-95-7039 TCGA-95-7944 TCGA-95-7947 
          44          218          127           34          377          477 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 
         830           84          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-L9-A7SV TCGA-MN-A4N1 TCGA-MP-A4T4 TCGA-MP-A4T7 
         578          435          111          827         1954         1954 
TCGA-MP-A4T9 TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1980         1971         1490          121 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 1 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             2370              6443 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            451.5             487.5 
[1] "2.0 - 2370.0 (451.5)" "1.0 - 6443.0 (487.5)"
[1] "hr=" "1.4"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  8Q GAIN MUTATED         2       52       66        23        34         35
  8Q GAIN WILD-TYPE       3       64       66        26        36         33
                   vv
clus                STAGE IIIB STAGE IV
  8Q GAIN MUTATED            7       10
  8Q GAIN WILD-TYPE          4       14
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                52                64
  STAGE IB                66                66
  STAGE IIA               23                26
  STAGE IIB               34                36
  STAGE IIIA              35                33
  STAGE IIIB               7                 4
  STAGE IV                10                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
  8Q GAIN MUTATED    63 133  24   7
  8Q GAIN WILD-TYPE  84 134  18  11
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              63                84
  T2             133               134
  T3              24                18
  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   147  37    40
  8Q GAIN WILD-TYPE 154  54    34
D16V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                147               154
  N1                 37                54
  N2+N3              40                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   155   8   0   2  62
  8Q GAIN WILD-TYPE 171  10   1   2  61
D16V6, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              155               171
  M1                8                10
  M1A               0                 1
  M1B               2                 2
  MX               62                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"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   119 110
  8Q GAIN WILD-TYPE 136 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    119  110
  8Q GAIN WILD-TYPE  136  111
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             119               136
  MALE               110               111
[1] 2 2
[1] FALSE
D16V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8Q GAIN MUTATED                           10
  8Q GAIN WILD-TYPE                          5
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8Q GAIN MUTATED                                  45
  8Q GAIN WILD-TYPE                                49
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                  152
  8Q GAIN WILD-TYPE                                                151
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8Q GAIN MUTATED                                            0
  8Q GAIN WILD-TYPE                                          5
                   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                                               3
  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                                      10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             152
  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                    3
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   8Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               151
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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    11 218
  8Q GAIN WILD-TYPE  10 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     11  218
  8Q GAIN WILD-TYPE   10  237
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               11                10
  YES             218               237
[1] 2 2
[1] FALSE
D16V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   154   8   3  10
  8Q GAIN WILD-TYPE 173   4   1  11
D16V12, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             154               173
  R1               8                 4
  R2               3                 1
  RX              10                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
  8Q GAIN MUTATED                                  0     5
  8Q GAIN WILD-TYPE                                1     1
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          17   176
  8Q GAIN WILD-TYPE                        18   191
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                     17                18
  WHITE                                        176               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"
D16V14, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3 162
  8Q GAIN WILD-TYPE   4 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  162
  8Q GAIN WILD-TYPE    4  183
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             162               183
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    35   6
  9P GAIN WILD-TYPE 294  81
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               41               375 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6                81 
$`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-49-AARQ TCGA-50-5051 TCGA-50-6597 TCGA-55-6972 TCGA-55-7903 
         337         6443          455         1015         1475           19 
TCGA-55-7995 TCGA-55-8301 TCGA-55-8514 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A4DF 
           5           44          202           66           29           47 
TCGA-64-5775 TCGA-69-7973 TCGA-69-7979 TCGA-69-8253 TCGA-69-A59K TCGA-73-4659 
          62          230           89          100          214          711 
TCGA-73-4666 TCGA-73-7499 TCGA-78-7163 TCGA-78-8662 TCGA-80-5608 TCGA-86-7953 
         800          519         1950         1964         1972          591 
TCGA-86-8669 TCGA-91-6828 TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VN 
          34          323           34         1973          477          553 
TCGA-97-7553 TCGA-97-7554 TCGA-L9-A444 TCGA-MP-A4TC TCGA-S2-AA1A 
        1332          775            6         1944          121 

$`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          705           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          462          100            6          600           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-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
         674          216           23           29           11            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
          15          228            9            3          146          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-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
          48         1952            1           28            5          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-64-1676 TCGA-64-1677 TCGA-64-1678 
        2199         1246          910         1728          628         1189 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
        1686         1126         1968         1959         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-69-7974 TCGA-69-7978 TCGA-69-7980 
         690          414          165          184           70          382 
TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 
          77          129           61         1600          912          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS 
         131           40          164           38          621          305 
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-78-7154 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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
         215         1940         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-83-5908 
        1949         1971         1981         1954         1965          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 
        1959           11          630          422         1968         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-86-8280 TCGA-86-8281 
         479          489          476          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-91-6829 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          505          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-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
           2          568          377          476          830           84 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 
         121          605          964         1965         1932          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-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
         266          312          111          102          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
          84         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-A4TK TCGA-MP-A5C7 
        1955         1971         1490 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                5                 1 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             6443              2696 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              477               476 
[1] "5.0 - 6443.0 (477.0)" "1.0 - 2696.0 (476.0)"
[1] "hr=" "1.5"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  9P GAIN MUTATED         1       13       12         2         6          7
  9P GAIN WILD-TYPE       4      103      120        47        64         61
                   vv
clus                STAGE IIIB STAGE IV
  9P GAIN MUTATED            1        3
  9P GAIN WILD-TYPE         10       21
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                13               103
  STAGE IB                12               120
  STAGE IIA                2                47
  STAGE IIB                6                64
  STAGE IIIA               7                61
  STAGE IIIB               1                10
  STAGE IV                 3                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    19  20   5   1
  9P GAIN WILD-TYPE 128 247  37  17
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1              19               128
  T2              20               247
  T3               5                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
  9P GAIN MUTATED    30   6     8
  9P GAIN WILD-TYPE 271  85    66
D17V5, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0                 30               271
  N1                  6                85
  N2+N3               8                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
  9P GAIN MUTATED    31   1   0   2  11
  9P GAIN WILD-TYPE 295  17   1   2 112
D17V6, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               31               295
  M1                1                17
  M1A               0                 1
  M1B               2                 2
  MX               11               112
[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    29  16
  9P GAIN WILD-TYPE 226 205
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     29   16
  9P GAIN WILD-TYPE  226  205
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              29               226
  MALE                16               205
[1] 2 2
[1] FALSE
D17V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9P GAIN MUTATED                            1
  9P GAIN WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9P GAIN MUTATED                                  11
  9P GAIN WILD-TYPE                                83
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                   26
  9P GAIN WILD-TYPE                                                277
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9P GAIN MUTATED                                            1
  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                                               1
  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)              26
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  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                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   9P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               277
  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  43
  9P GAIN WILD-TYPE  19 412
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   43
  9P GAIN WILD-TYPE   19  412
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                2                19
  YES              43               412
[1] 2 2
[1] FALSE
D17V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    30   1   1   3
  9P GAIN WILD-TYPE 297  11   3  18
D17V12, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              30               297
  R1               1                11
  R2               1                 3
  RX               3                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
  9P GAIN MUTATED                                  0     0
  9P GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           7    31
  9P GAIN WILD-TYPE                        28   336
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                      7                28
  WHITE                                         31               336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  37
  9P GAIN WILD-TYPE   7 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   37
  9P GAIN WILD-TYPE    7  308
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              37               308
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    26   5
  9Q GAIN WILD-TYPE 303  82
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               31               385 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5                82 
$`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          600           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-95-7562 TCGA-95-7947 TCGA-95-A4VN TCGA-97-7553 TCGA-MN-A4N5 TCGA-MP-A4TC 
        1973          477          553         1332           84         1944 
TCGA-S2-AA1A 
         121 

$`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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
         522          354         6443         2174         2146          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-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        2370          653          567          883          764          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-55-1596 TCGA-55-5899 TCGA-55-6543 
         701         1178         1479         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          705           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-55-8085 TCGA-55-8087 
         197           21            3           31           33          462 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
         100            6           26            4           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
          33           46           66          674          216           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-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 
          49          106           33           42           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-62-8397 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-64-5775 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-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
          89          382           77          129          214           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        1600          711          912          467          131           40 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 
         164           38          621          305         1970         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-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
        1963         1221          215         1940         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-78-7633 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-86-7713 
        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-86-8278 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         1955           19           26           35           45 
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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
          79          372          842          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         505          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
         127          186           34            2          568          377 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 
         476          830           84          121          605          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-L9-A50W 
         238          578          435          116            6          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV 
         312          111          102          827         1175         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-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1970         1970          142         1955         1971 
TCGA-MP-A5C7 
        1490 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                5                 1 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1973              6443 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              591               462 
[1] "5.0 - 1973.0 (591.0)" "1.0 - 6443.0 (462.0)"
[1] "hr=" "1.1"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  9Q GAIN MUTATED         0        8       12         2         4          2
  9Q GAIN WILD-TYPE       5      108      120        47        66         66
                   vv
clus                STAGE IIIB STAGE IV
  9Q GAIN MUTATED            1        4
  9Q GAIN WILD-TYPE         10       20
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 8               108
  STAGE IB                12               120
  STAGE IIA                2                47
  STAGE IIB                4                66
  STAGE IIIA               2                66
  STAGE IIIB               1                10
  STAGE IV                 4                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    13  17   2   1
  9Q GAIN WILD-TYPE 134 250  40  17
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              13               134
  T2              17               250
  T3               2                40
  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    21   6     5
  9Q GAIN WILD-TYPE 280  85    69
D18V5, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0                 21               280
  N1                  6                85
  N2+N3               5                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
  9Q GAIN MUTATED    23   2   0   2   6
  9Q GAIN WILD-TYPE 303  16   1   2 117
D18V6, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               23               303
  M1                2                16
  M1A               0                 1
  M1B               2                 2
  MX                6               117
[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    19  14
  9Q GAIN WILD-TYPE 236 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     19   14
  9Q GAIN WILD-TYPE  236  207
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              19               236
  MALE                14               207
[1] 2 2
[1] FALSE
D18V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9Q GAIN MUTATED                            0
  9Q GAIN WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9Q GAIN MUTATED                                   7
  9Q GAIN WILD-TYPE                                87
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                   22
  9Q GAIN WILD-TYPE                                                281
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9Q GAIN MUTATED                                            1
  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                                               1
  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)              22
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       1
  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                    1
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   9Q GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 87
  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                                 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  32
  9Q GAIN WILD-TYPE  20 423
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   32
  9Q GAIN WILD-TYPE   20  423
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                20
  YES              32               423
[1] 2 2
[1] FALSE
D18V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    23   1   0   2
  9Q GAIN WILD-TYPE 304  11   4  19
D18V12, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              23               304
  R1               1                11
  R2               0                 4
  RX               2                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
  9Q GAIN MUTATED                                  0     0
  9Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           4    25
  9Q GAIN WILD-TYPE                        31   342
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                      4                31
  WHITE                                         25               342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  26
  9Q GAIN WILD-TYPE   7 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   26
  9Q GAIN WILD-TYPE    7  319
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              26               319
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    80  18
  10P GAIN WILD-TYPE 249  69
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                98                318 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                18                 69 
$`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-55-7907 TCGA-55-7910 
         424          993         1475           35           16          197 
TCGA-55-8092 TCGA-55-8205 TCGA-55-8302 TCGA-55-8511 TCGA-55-8615 TCGA-55-8620 
          26           33           23            9           15           66 
TCGA-55-A491 TCGA-62-8398 TCGA-64-1678 TCGA-69-7763 TCGA-69-7979 TCGA-71-6725 
        1952         1970         1189          690           89           61 
TCGA-73-4658 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-A9RS TCGA-75-6214 
        1600          131           40           38          305         1970 
TCGA-75-7027 TCGA-78-7149 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 
        1956         1093         1948         1957         1221          678 
TCGA-78-7161 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8662 TCGA-80-5608 
         215          327         1952          994         1964         1972 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7955 TCGA-86-8358 TCGA-86-8672 
          11          630          422          508           19           15 
TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6836 TCGA-91-7771 
         455           10           30         1940          417          492 
TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7553 
         186          568          377          553          605         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8179 TCGA-99-8025 TCGA-J2-8194 TCGA-L9-A443 
         775          181           15          427          114          116 
TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T7 
           6          111          827         1175           84         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-49-AARQ TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 
         522          354         6443         2174          785          944 
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-50-6597 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ 
         883          764         1015          105         1971          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
         701         1178         1479         1375           87            2 
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-55-7284 TCGA-55-7570 TCGA-55-7573 
        2151         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          705           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          24           54           19           21            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33          462          100            6          600 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
           4           47           15           46           66          674 
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 
         505          174           36           44          218          297 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
         127           34            2         1973          477          476 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         830           84          121          964         1965         1932 
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-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
         148          115          197          271          392          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
          44          170          154          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MP-A4SV 
         578          435          266          312          102         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 TCGA-S2-AA1A 
        1970          142         1955         1971         1490          121 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                  1 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              2370               6443 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             560.5              460.5 
[1] "6.0 - 2370.0 (560.5)" "1.0 - 6443.0 (460.5)"
[1] "hr=" "1.3"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  10P GAIN MUTATED         1       23       32        12        13         15
  10P GAIN WILD-TYPE       4       93      100        37        57         53
                    vv
clus                 STAGE IIIB STAGE IV
  10P GAIN MUTATED            4        7
  10P GAIN WILD-TYPE          7       17
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 23                 93
  STAGE IB                 32                100
  STAGE IIA                12                 37
  STAGE IIB                13                 57
  STAGE IIIA               15                 53
  STAGE IIIB                4                  7
  STAGE IV                  7                 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
  10P GAIN MUTATED    22  68  12   5
  10P GAIN WILD-TYPE 125 199  30  13
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               22                125
  T2               68                199
  T3               12                 30
  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    76  13    17
  10P GAIN WILD-TYPE 225  78    57
D19V5, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                  76                225
  N1                  13                 78
  N2+N3               17                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  10P GAIN MUTATED    76   6   0   1  24
  10P GAIN WILD-TYPE 250  12   1   3  99
D19V6, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                76                250
  M1                 6                 12
  M1A                0                  1
  M1B                1                  3
  MX                24                 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"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    43  64
  10P GAIN WILD-TYPE 212 157
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     43   64
  10P GAIN WILD-TYPE  212  157
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               43                212
  MALE                 64                157
[1] 2 2
[1] FALSE
D19V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10P GAIN MUTATED                            4
  10P GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10P GAIN MUTATED                                  24
  10P GAIN WILD-TYPE                                70
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                   66
  10P GAIN WILD-TYPE                                                237
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10P GAIN MUTATED                                            0
  10P GAIN WILD-TYPE                                          5
                    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                                               1
  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                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               66
  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                     1
  MUCINOUS (COLLOID) CARCINOMA                                      0
                                                    clus
vv                                                   10P GAIN WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                237
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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     2 105
  10P GAIN WILD-TYPE  19 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2  105
  10P GAIN WILD-TYPE   19  350
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                 19
  YES              105                350
[1] 2 2
[1] FALSE
D19V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    72   3   0   8
  10P GAIN WILD-TYPE 255   9   4  13
D19V12, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               72                255
  R1                3                  9
  R2                0                  4
  RX                8                 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
  10P GAIN MUTATED                                  0     3
  10P GAIN WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           8    75
  10P GAIN WILD-TYPE                        27   292
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                       8                 27
  WHITE                                          75                292
[1] 4 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  69
  10P GAIN WILD-TYPE   5 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   69
  10P GAIN WILD-TYPE    5  276
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               69                276
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    55  14
  10Q GAIN WILD-TYPE 274  73
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                69                347 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                 73 
$`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-55-7907 TCGA-55-8205 TCGA-55-8302 TCGA-55-8615 TCGA-55-A491 TCGA-62-8398 
          16           33           23           15         1952         1970 
TCGA-69-7763 TCGA-71-6725 TCGA-73-4658 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
         690           61         1600          131           40           38 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 
        1970         1956         1093         1948         1221          678 
TCGA-78-7161 TCGA-78-8662 TCGA-86-7701 TCGA-86-7713 TCGA-86-8279 TCGA-86-8358 
         215         1964           11          422          482           19 
TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-7771 TCGA-95-7567 
          15          455           10           30          492          568 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8179 
          84          605         1332          775          181           15 
TCGA-99-8025 TCGA-J2-8194 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T7 
         427          114          111         1175           84         1954 
TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A5C7 
        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-49-AARQ TCGA-50-5045 
         369          890          522          354         6443         2174 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
         785          944          246          282          267         1091 
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-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
         105         1971          424          280          701         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 
        1479         1375           87            2           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-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          18          121            6            4           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
         705           39           39           34           24           54 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
          19          197           21            3           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33          462          100            6          600           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
           4           47           15           46           66          674 
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-55-8614 
         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-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-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U 
         162         1216         1289         2696         1445         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
        2199         1246          910         1728          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-67-3772 
         864         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-69-7764 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-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-7498 
         711          912          800          467          164          621 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
         519          305         1967         1965         1973         1988 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        1950         1944         1963         1202          760         1957 
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-78-7539 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-86-7711 TCGA-86-7714 
        1965         1972          824         1959          630         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
         591         1963          508          745           10         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
          13           24          479          489          476           16 
TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
        1955           26           35           45           34           18 
TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
         405           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-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
          35          505          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
         297          127          186           34            2         1973 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
         377          477          476          830          121          553 
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-L9-A443 
         287          282          238          578          435          116 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MP-A4SV 
           6          266          312          102          827         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-S2-AA1A 
        1970          142         1955         1971          121 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                  1 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              2370               6443 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               605                459 
[1] "10.0 - 2370.0 (605.0)" "1.0 - 6443.0 (459.0)" 
[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         8         9         15
  10Q GAIN WILD-TYPE       5       99      113        41        61         53
                    vv
clus                 STAGE IIIB STAGE IV
  10Q GAIN MUTATED            3        6
  10Q GAIN WILD-TYPE          8       18
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 17                 99
  STAGE IB                 19                113
  STAGE IIA                 8                 41
  STAGE IIB                 9                 61
  STAGE IIIA               15                 53
  STAGE IIIB                3                  8
  STAGE IV                  6                 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
  10Q GAIN MUTATED    16  48   9   4
  10Q GAIN WILD-TYPE 131 219  33  14
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               16                131
  T2               48                219
  T3                9                 33
  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  10    17
  10Q GAIN WILD-TYPE 252  81    57
D20V5, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                  49                252
  N1                  10                 81
  N2+N3               17                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  10Q GAIN MUTATED    56   6   0   0  15
  10Q GAIN WILD-TYPE 270  12   1   4 108
D20V6, multiclass
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                56                270
  M1                 6                 12
  M1A                0                  1
  M1B                0                  4
  MX                15                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"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    29  48
  10Q GAIN WILD-TYPE 226 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     29   48
  10Q GAIN WILD-TYPE  226  173
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               29                226
  MALE                 48                173
[1] 2 2
[1] FALSE
D20V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10Q GAIN MUTATED                            3
  10Q GAIN WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10Q GAIN MUTATED                                  19
  10Q GAIN WILD-TYPE                                75
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                   45
  10Q GAIN WILD-TYPE                                                258
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10Q GAIN MUTATED                                            0
  10Q GAIN WILD-TYPE                                          5
                    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                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  10Q GAIN MUTATED                              0
  10Q GAIN WILD-TYPE                            7
D20V9, multiclass
                                                    clus
vv                                                   10Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               45
  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                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  75
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                258
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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                       5
  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  75
  10Q GAIN WILD-TYPE  19 380
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   75
  10Q GAIN WILD-TYPE   19  380
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 2                 19
  YES               75                380
[1] 2 2
[1] FALSE
D20V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    53   2   0   5
  10Q GAIN WILD-TYPE 274  10   4  16
D20V12, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               53                274
  R1                2                 10
  R2                0                  4
  RX                5                 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
  10Q GAIN MUTATED                                  0     2
  10Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           4    56
  10Q GAIN WILD-TYPE                        31   311
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                       4                 31
  WHITE                                          56                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"
D20V14, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1  50
  10Q GAIN WILD-TYPE   6 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   50
  10Q GAIN WILD-TYPE    6  295
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               50                295
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    62  19
  11P GAIN WILD-TYPE 267  68
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                81                335 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                19                 68 
$`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-44-7660 TCGA-44-7661 TCGA-44-7669 
         705         1864         1978          592          366         1970 
TCGA-44-7670 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4512 
         882           99          486          466          287          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-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-7995 TCGA-55-8092 
        1375            2           24           25            5           26 
TCGA-55-8096 TCGA-55-8205 TCGA-55-8514 TCGA-55-8620 TCGA-55-A494 TCGA-55-A4DF 
          47           33          202           66            5           47 
TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 
        2696         1445          628         1968           62          864 
TCGA-67-3770 TCGA-67-3771 TCGA-67-6215 TCGA-69-7973 TCGA-69-7974 TCGA-71-6725 
          31          610          174          230          184           61 
TCGA-73-4662 TCGA-75-6214 TCGA-78-7163 TCGA-78-7167 TCGA-78-7542 TCGA-78-8655 
         912         1970         1950         1937         1952         1981 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7955 TCGA-86-8278 TCGA-86-8280 TCGA-86-A4P7 
        1972         1959          508          476           16           14 
TCGA-91-6829 TCGA-91-6840 TCGA-91-6848 TCGA-93-7348 TCGA-95-7043 TCGA-95-7562 
        1940          372          224          127            2         1973 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8177 TCGA-99-8033 TCGA-L9-A443 TCGA-MN-A4N4 
         775          181          147          170          116         1175 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-S2-AA1A 
        1951         1944          121 

$`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-44-7662 TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 
        1942          444          218          557          535          719 
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-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
         896         1700          445          890          522          354 
TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        6443         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-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 
        1986         1971          280         1479           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          705           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          462          100            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
         600            4           15           46           66          674 
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-55-8614 
          15          228            9            3          146          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-A4DG 
          29           48         1952            1           28          162 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1216         1289         1970         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
         910         1728         1189         1686         1126         1959 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        1305         1559          866          573          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-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         165           70           89          382          100           77 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
         129          214         1600          711          800          467 
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-73-A9RS TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 
         305         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-78-7154 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-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
         215         1940         1934         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-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 
        1954         1964         1965          824           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
         422         1968          591         1963          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 
        1963           13           24          479          489          482 
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-A456 TCGA-86-A4D0 
          18           15          455          405           10           30 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          39          323           60          310           79          417 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         842           35          492          505          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 
          44          218          297          186           34          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
         377          477          476          830           84          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         553          605          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-L9-A50W TCGA-L9-A743 
         238          578          435            6          266          312 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         111          102          827           84         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE 
        1951         1954         1954         1957         1980         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970          142         1955         1971         1490 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                  1 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              2696               6443 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               476                476 
[1] "2.0 - 2696.0 (476.0)" "1.0 - 6443.0 (476.0)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  11P GAIN MUTATED         0       21       24         6        13         18
  11P GAIN WILD-TYPE       5       95      108        43        57         50
                    vv
clus                 STAGE IIIB STAGE IV
  11P GAIN MUTATED            4        5
  11P GAIN WILD-TYPE          7       19
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 21                 95
  STAGE IB                 24                108
  STAGE IIA                 6                 43
  STAGE IIB                13                 57
  STAGE IIIA               18                 50
  STAGE IIIB                4                  7
  STAGE IV                  5                 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
  11P GAIN MUTATED    28  52   4   5
  11P GAIN WILD-TYPE 119 215  38  13
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               28                119
  T2               52                215
  T3                4                 38
  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    53  15    20
  11P GAIN WILD-TYPE 248  76    54
D21V5, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                  53                248
  N1                  15                 76
  N2+N3               20                 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
  11P GAIN MUTATED    59   4   0   1  26
  11P GAIN WILD-TYPE 267  14   1   3  97
D21V6, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                59                267
  M1                 4                 14
  M1A                0                  1
  M1B                1                  3
  MX                26                 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"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    56  35
  11P GAIN WILD-TYPE 199 186
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     56   35
  11P GAIN WILD-TYPE  199  186
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               56                199
  MALE                 35                186
[1] 2 2
[1] FALSE
D21V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11P GAIN MUTATED                            2
  11P GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11P GAIN MUTATED                                  16
  11P GAIN WILD-TYPE                                78
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                   61
  11P GAIN WILD-TYPE                                                242
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11P GAIN MUTATED                                            2
  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                                             5
                    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)               61
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  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                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                242
  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                       5
  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  88
  11P GAIN WILD-TYPE  18 367
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3   88
  11P GAIN WILD-TYPE   18  367
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 3                 18
  YES               88                367
[1] 2 2
[1] FALSE
D21V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    61   2   1   4
  11P GAIN WILD-TYPE 266  10   3  17
D21V12, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               61                266
  R1                2                 10
  R2                1                  3
  RX                4                 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
  11P GAIN MUTATED                                  0     2
  11P GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           8    67
  11P GAIN WILD-TYPE                        27   300
D21V13, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                       8                 27
  WHITE                                          67                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"
D21V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2  65
  11P GAIN WILD-TYPE   5 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   65
  11P GAIN WILD-TYPE    5  280
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               65                280
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    77  25
  11Q GAIN WILD-TYPE 252  62
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               102                314 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                25                 62 
$`11Q GAIN MUTATED`
TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 TCGA-05-4432 
        1958         1997          455          912          669          761 
TCGA-05-5423 TCGA-05-5429 TCGA-38-4628 TCGA-38-4629 TCGA-38-4632 TCGA-44-2656 
         151           30         1492          864         1357         1429 
TCGA-44-2659 TCGA-44-2662 TCGA-44-5645 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 
        1367         1280          383          658          705         1864 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 
        1978          592          366          218         1970          882 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4512 
         385           99          486          466          287          157 
TCGA-49-6743 TCGA-50-5933 TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 
         369         2370         1015         1986          424          701 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-7910 
        1178         1375            2           24           25          197 
TCGA-55-7994 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8506 TCGA-55-8510 
          31           26           47           33           11          228 
TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
         202           48           66            5           47          162 
TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 
        2696         1445          628         1968           62          864 
TCGA-67-3770 TCGA-67-3771 TCGA-67-6215 TCGA-69-7973 TCGA-69-7974 TCGA-69-A59K 
          31          610          174          230          184          214 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-78-7154 
          61         1600          800          467          164         1948 
TCGA-78-7155 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-8655 TCGA-78-8662 
        1957         1950         1937         1972         1981         1964 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7955 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        1972         1959          508          476          482           16 
TCGA-86-8359 TCGA-86-A4P7 TCGA-91-6829 TCGA-91-6840 TCGA-91-6848 TCGA-91-A4BC 
          26           14         1940          372          224           44 
TCGA-93-7348 TCGA-95-7043 TCGA-95-7562 TCGA-97-7553 TCGA-97-7937 TCGA-97-8177 
         127            2         1973         1332          181          147 
TCGA-99-8033 TCGA-L9-A443 TCGA-MN-A4N4 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-S2-AA1A 
         170          116         1175         1951         1944          121 

$`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-05-4422 TCGA-05-4424 TCGA-05-4426 
        1431          578          610          365          913          791 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 
         791          761          730          457          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-38-6178 TCGA-38-7271 
        1962         1147         1073          354          448         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-44-3918 TCGA-44-3919 TCGA-44-4112 
         246         1130         1163         1036          190          722 
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-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7667 TCGA-44-7671 
         704         1938         1942          444          557          535 
TCGA-44-7672 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
         719          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-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
         896         1700          445          890          522          354 
TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        6443         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          705           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          462          100            6          600            4 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          15           46           66          674          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 
          23           29            8           15            9            3 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
         146          536           15           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-62-8398 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1216         1289         1970         2067         2199         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
         910         1728         1189         1686         1126         1959 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        1305         1559          866          573          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-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         165           70           89          382          100           77 
TCGA-69-8255 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
         129          711          912          131           40           38 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
         621          519          305         1970         1967         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        1965         1973         1988         1950         1944         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1963         1202          760         1961         1963         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 
         678          215         1940         1934         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-78-8660 TCGA-80-5607 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 
        1971         1954         1965          824           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
         422         1968          591         1963          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8281 
        1963           13           24          479          489         1955 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          19           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-A4BD TCGA-93-7347 
         492          505          174           36          218          297 
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-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
         830           84          121          553          605          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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
           6          266          312          111          102          827 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
          84         1946         1967         1951         1954         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 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                  1 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              2696               6443 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             471.5              476.5 
[1] "2.0 - 2696.0 (471.5)" "1.0 - 6443.0 (476.5)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  11Q GAIN MUTATED         0       19       34        10        18         18
  11Q GAIN WILD-TYPE       5       97       98        39        52         50
                    vv
clus                 STAGE IIIB STAGE IV
  11Q GAIN MUTATED            4        9
  11Q GAIN WILD-TYPE          7       15
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 19                 97
  STAGE IB                 34                 98
  STAGE IIA                10                 39
  STAGE IIB                18                 52
  STAGE IIIA               18                 50
  STAGE IIIB                4                  7
  STAGE IV                  9                 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
  11Q GAIN MUTATED    28  67  10   5
  11Q GAIN WILD-TYPE 119 200  32  13
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               28                119
  T2               67                200
  T3               10                 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
  11Q GAIN MUTATED    68  20    21
  11Q GAIN WILD-TYPE 233  71    53
D22V5, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                  68                233
  N1                  20                 71
  N2+N3               21                 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
  11Q GAIN MUTATED    70   7   0   2  32
  11Q GAIN WILD-TYPE 256  11   1   2  91
D22V6, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                70                256
  M1                 7                 11
  M1A                0                  1
  M1B                2                  2
  MX                32                 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"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    65  47
  11Q GAIN WILD-TYPE 190 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     65   47
  11Q GAIN WILD-TYPE  190  174
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               65                190
  MALE                 47                174
[1] 2 2
[1] FALSE
D22V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11Q GAIN MUTATED                            1
  11Q GAIN WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11Q GAIN MUTATED                                  18
  11Q GAIN WILD-TYPE                                76
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                   81
  11Q GAIN WILD-TYPE                                                222
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11Q GAIN MUTATED                                            2
  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                                             5
                    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                                18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               81
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  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                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                222
  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                       5
  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     6 106
  11Q GAIN WILD-TYPE  15 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6  106
  11Q GAIN WILD-TYPE   15  349
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 6                 15
  YES              106                349
[1] 2 2
[1] FALSE
D22V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    73   3   1   5
  11Q GAIN WILD-TYPE 254   9   3  16
D22V12, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               73                254
  R1                3                  9
  R2                1                  3
  RX                5                 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
  11Q GAIN MUTATED                                  1     2
  11Q GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                          12    82
  11Q GAIN WILD-TYPE                        23   285
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                      12                 23
  WHITE                                          82                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"
D22V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     3  82
  11Q GAIN WILD-TYPE   4 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3   82
  11Q GAIN WILD-TYPE    4  263
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               82                263
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    90  23
  12P GAIN WILD-TYPE 239  64
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               113                303 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                23                 64 
$`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-49-4512 TCGA-49-6742 
         882          719           99          466          157          445 
TCGA-50-5045 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 TCGA-55-1594 
        2174          246          267          567          764         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6980 
        1479         1375          993           24           25           67 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7284 TCGA-55-7576 TCGA-55-7726 TCGA-55-7728 
        1233         1170          121           40           39           24 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8089 TCGA-55-8094 
          16          197           21            5          100            4 
TCGA-55-8096 TCGA-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
          47          674           23           29            8           15 
TCGA-55-8615 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 
          15           48           28            5           47         1970 
TCGA-62-8402 TCGA-62-A471 TCGA-64-1678 TCGA-64-1681 TCGA-64-5775 TCGA-67-3774 
        1445         1246         1189         1968           62          385 
TCGA-69-7973 TCGA-69-7980 TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
         230          382          214          800          131           40 
TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7154 TCGA-78-7159 
        1956         1973         1988         1944         1948         1221 
TCGA-78-7167 TCGA-78-7220 TCGA-78-8655 TCGA-86-6851 TCGA-86-7713 TCGA-86-7953 
        1937         1965         1981         1959          422          591 
TCGA-86-7954 TCGA-86-8278 TCGA-86-8280 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 
        1963          476           16           35           34           30 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 
         323         1940          417          372          224           36 
TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-95-A4VP TCGA-97-8552 
         186          568          377           84          605          115 
TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MN-A4N4 
         271           44          170          116          827         1175 
TCGA-MP-A4SV TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TI TCGA-S2-AA1A 
        1946         1954         1970         1955          121 

$`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-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         268          896         1700          369          890          522 
TCGA-49-6761 TCGA-49-AARQ TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         354         6443         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          705           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          462            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
         600           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-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7147 
         519          305         1970         1967         1965         1950 
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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1963          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-78-8660 TCGA-78-8662 TCGA-80-5607 
         994         1949         1971         1954         1964         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-86-8054 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-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
         489          482         1955           19           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-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 
          39           60          310           79          842           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         492          505          174           44          218          297 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
         127           34            2         1973          477          476 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         830          121          553          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-L9-A50W 
         282          238          578          435            6          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 
         312          111          102           84         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1971         1490 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                  1 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              2174               6443 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               445                486 
[1] "4.0 - 2174.0 (445.0)" "1.0 - 6443.0 (486.0)"
[1] "hr=" "1"  
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  12P GAIN MUTATED         2       31       29        19        14         25
  12P GAIN WILD-TYPE       3       85      103        30        56         43
                    vv
clus                 STAGE IIIB STAGE IV
  12P GAIN MUTATED            2       10
  12P GAIN WILD-TYPE          9       14
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 31                 85
  STAGE IB                 29                103
  STAGE IIA                19                 30
  STAGE IIB                14                 56
  STAGE IIIA               25                 43
  STAGE IIIB                2                  9
  STAGE IV                 10                 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    40  76  11   4
  12P GAIN WILD-TYPE 107 191  31  14
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               40                107
  T2               76                191
  T3               11                 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
  12P GAIN MUTATED    79  24    26
  12P GAIN WILD-TYPE 222  67    48
D23V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                  79                222
  N1                  24                 67
  N2+N3               26                 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
  12P GAIN MUTATED    87   8   0   2  34
  12P GAIN WILD-TYPE 239  10   1   2  89
D23V6, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                87                239
  M1                 8                 10
  M1A                0                  1
  M1B                2                  2
  MX                34                 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"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    65  67
  12P GAIN WILD-TYPE 190 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     65   67
  12P GAIN WILD-TYPE  190  154
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               65                190
  MALE                 67                154
[1] 2 2
[1] FALSE
D23V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12P GAIN MUTATED                            3
  12P GAIN WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12P GAIN MUTATED                                  23
  12P GAIN WILD-TYPE                                71
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                   92
  12P GAIN WILD-TYPE                                                211
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12P GAIN MUTATED                                            1
  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                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  12P GAIN MUTATED                              3
  12P GAIN WILD-TYPE                            4
D23V9, multiclass
                                                    clus
vv                                                   12P GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                23
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               92
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  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                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                211
  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                       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"
D23V10, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     5 127
  12P GAIN WILD-TYPE  16 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5  127
  12P GAIN WILD-TYPE   16  328
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 5                 16
  YES              127                328
[1] 2 2
[1] FALSE
D23V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    93   3   2   6
  12P GAIN WILD-TYPE 234   9   2  15
D23V12, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               93                234
  R1                3                  9
  R2                2                  2
  RX                6                 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
  12P GAIN MUTATED                                  0     3
  12P GAIN WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          11    99
  12P GAIN WILD-TYPE                        24   268
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                      11                 24
  WHITE                                          99                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"
D23V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1  93
  12P GAIN WILD-TYPE   6 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   93
  12P GAIN WILD-TYPE    6  252
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               93                252
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    87  19
  12Q GAIN WILD-TYPE 242  68
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               106                310 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                19                 68 
$`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-49-4512 
         719           99          486          466          287          157 
TCGA-49-6742 TCGA-50-5045 TCGA-50-5051 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 
         445         2174          455          246          267          567 
TCGA-50-5944 TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 
         764          424         1178         1479         1375          993 
TCGA-55-6712 TCGA-55-6971 TCGA-55-6987 TCGA-55-7284 TCGA-55-7726 TCGA-55-7728 
          24           25         1170          121           39           24 
TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 TCGA-55-8089 TCGA-55-8208 TCGA-55-8302 
          54          197           21          100          674           23 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 TCGA-55-A490 TCGA-55-A491 
          29            8           15           15           48         1952 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-62-A46V 
          28            5           47         1970         1445         2199 
TCGA-62-A471 TCGA-64-1678 TCGA-64-1681 TCGA-64-5779 TCGA-67-3774 TCGA-69-7973 
        1246         1189         1968          864          385          230 
TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
         382          129          214          800          131           40 
TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7167 TCGA-78-7220 
        1956         1973         1988         1944         1937         1965 
TCGA-78-8655 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
        1981         1959           11          422          591         1963 
TCGA-86-8278 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 
         476           19           35           34           30          323 
TCGA-91-6836 TCGA-91-6840 TCGA-93-8067 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 
         417          372          186          568          377           84 
TCGA-95-A4VP TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A443 
         605          115          271           44          170          116 
TCGA-MP-A4SV TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TI 
        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-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
         896         1700          369          890          522          354 
TCGA-49-AARQ TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
        6443         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          705           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          462 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
           6          600           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-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7147 
         519          305         1970         1967         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-78-7158 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-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1950         1934         1972         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-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7711 TCGA-86-7714 
        1964         1965         1972          824          630         1968 
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-86-8359 
         479          489          482           16         1955           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-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
          14           39         1940           60          310           79 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         842          224           35          492          505          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 
          36           44          218          297          127           34 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
           2         1973          477          476          830          121 
TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         553          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-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 
         147           15          148          197          392          427 
TCGA-99-8028 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         459          154          114          287          282          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
         578          435            6          266          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 
         102          827         1175           84         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF 
        1954         1957         1980         1951         1944         1970 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
         142         1971         1490          121 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                  1 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              2199               6443 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             456.0              480.5 
[1] "5.0 - 2199.0 (456.0)" "1.0 - 6443.0 (480.5)"
[1] "hr=" "1.4"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  12Q GAIN MUTATED         2       28       31        15        15         22
  12Q GAIN WILD-TYPE       3       88      101        34        55         46
                    vv
clus                 STAGE IIIB STAGE IV
  12Q GAIN MUTATED            3        9
  12Q GAIN WILD-TYPE          8       15
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 28                 88
  STAGE IB                 31                101
  STAGE IIA                15                 34
  STAGE IIB                15                 55
  STAGE IIIA               22                 46
  STAGE IIIB                3                  8
  STAGE IV                  9                 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    36  74  10   4
  12Q GAIN WILD-TYPE 111 193  32  14
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               36                111
  T2               74                193
  T3               10                 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
  12Q GAIN MUTATED    78  21    24
  12Q GAIN WILD-TYPE 223  70    50
D24V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                  78                223
  N1                  21                 70
  N2+N3               24                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  12Q GAIN MUTATED    83   8   0   1  32
  12Q GAIN WILD-TYPE 243  10   1   3  91
D24V6, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                83                243
  M1                 8                 10
  M1A                0                  1
  M1B                1                  3
  MX                32                 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"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    63  62
  12Q GAIN WILD-TYPE 192 159
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     63   62
  12Q GAIN WILD-TYPE  192  159
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               63                192
  MALE                 62                159
[1] 2 2
[1] FALSE
D24V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12Q GAIN MUTATED                            4
  12Q GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12Q GAIN MUTATED                                  22
  12Q GAIN WILD-TYPE                                72
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                   87
  12Q GAIN WILD-TYPE                                                216
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12Q GAIN MUTATED                                            0
  12Q GAIN WILD-TYPE                                          5
                    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                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  12Q GAIN MUTATED                              3
  12Q GAIN WILD-TYPE                            4
D24V9, multiclass
                                                    clus
vv                                                   12Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               87
  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                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  72
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                216
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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                       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"
D24V10, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     5 120
  12Q GAIN WILD-TYPE  16 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      5  120
  12Q GAIN WILD-TYPE   16  335
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 5                 16
  YES              120                335
[1] 2 2
[1] FALSE
D24V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    86   3   2   6
  12Q GAIN WILD-TYPE 241   9   2  15
D24V12, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               86                241
  R1                3                  9
  R2                2                  2
  RX                6                 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
  12Q GAIN MUTATED                                  0     3
  12Q GAIN WILD-TYPE                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           8    93
  12Q GAIN WILD-TYPE                        27   274
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                       8                 27
  WHITE                                          93                274
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     2  86
  12Q GAIN WILD-TYPE   5 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2   86
  12Q GAIN WILD-TYPE    5  259
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               86                259
[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 301  77
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                38                378 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                 77 
$`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-49-AARQ TCGA-50-5045 
         369          890          522          354         6443         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-50-7109 TCGA-50-8460 
         883          764          686         1015          255          105 
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-55-7283 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 
         705           39           34           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          462 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
           6          600           26            4           47           15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          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-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
          49          106           33           42           29           48 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
        1952           28            5           47          162         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-64-1679 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-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
         427          385          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-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
          89          382           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-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-7025 
          40          164          621          519          305         1967 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
        1965         1973         1988         1950         1944         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-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        1972         1949          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-86-8075 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-86-8673 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-91-6831 
          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          505          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
         297          127          186           34            2         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
         568          377          477          476          830           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 
         121          553          605          964         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-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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
         435          116            6          266          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 
         102          827         1175           84         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 TCGA-S2-AA1A 
        1970          142         1955         1971         1490          121 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                  2 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              1986               6443 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             608.5              460.5 
[1] "1.0 - 1986.0 (608.5)" "2.0 - 6443.0 (460.5)"
[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       5      108      121        42        64         65
                    vv
clus                 STAGE IIIB STAGE IV
  13Q GAIN MUTATED            1        6
  13Q GAIN WILD-TYPE         10       18
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  8                108
  STAGE IB                 11                121
  STAGE IIA                 7                 42
  STAGE IIB                 6                 64
  STAGE IIIA                3                 65
  STAGE IIIB                1                 10
  STAGE IV                  6                 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
  13Q GAIN MUTATED    14  26   1   1
  13Q GAIN WILD-TYPE 133 241  41  17
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               14                133
  T2               26                241
  T3                1                 41
  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 273  81    70
D25V5, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0                  28                273
  N1                  10                 81
  N2+N3                4                 70
[1] 3 2
[1] 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 296  13   1   3 117
D25V6, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                30                296
  M1                 5                 13
  M1A                0                  1
  M1B                1                  3
  MX                 6                117
[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 232 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     23   19
  13Q GAIN WILD-TYPE  232  202
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               23                232
  MALE                 19                202
[1] 2 2
[1] FALSE
D25V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  13Q GAIN MUTATED                            0
  13Q GAIN WILD-TYPE                         15
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  13Q GAIN MUTATED                                   9
  13Q GAIN WILD-TYPE                                85
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                   29
  13Q GAIN WILD-TYPE                                                274
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  13Q GAIN MUTATED                                            0
  13Q GAIN WILD-TYPE                                          5
                    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                                             5
                    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                                         15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                274
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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                       5
  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  19 415
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2   40
  13Q GAIN WILD-TYPE   19  415
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 2                 19
  YES               40                415
[1] 2 2
[1] FALSE
D25V11, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED    36   0   0   0
  13Q GAIN WILD-TYPE 291  12   4  21
D25V12, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               36                291
  R1                0                 12
  R2                0                  4
  RX                0                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    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                        31   336
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                 31
  WHITE                                          31                336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1  27
  13Q GAIN WILD-TYPE   6 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   27
  13Q GAIN WILD-TYPE    6  318
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               27                318
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    77  21
  14Q GAIN WILD-TYPE 252  66
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                98                318 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 66 
$`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-49-AARQ TCGA-50-5941 TCGA-50-5946 TCGA-50-7109 TCGA-53-A4EZ TCGA-55-5899 
        6443          567          686          255          280           87 
TCGA-55-6543 TCGA-55-6971 TCGA-55-6983 TCGA-55-7724 TCGA-55-7815 TCGA-55-7907 
           2           25         1826          705           54           16 
TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 TCGA-55-8091 TCGA-55-8096 TCGA-55-8206 
         197            5           33          600           47           46 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8614 TCGA-55-A490 
          23           11            8          228          536           48 
TCGA-55-A4DG TCGA-64-1677 TCGA-64-5774 TCGA-64-5775 TCGA-67-3770 TCGA-67-3771 
         162          628         1959           62           31          610 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-71-6725 TCGA-73-4658 
         690          230          184           89           61         1600 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4677 TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 
         711          800           38          519         1967         1965 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 
        1973         1944         1093         1221          215         1937 
TCGA-80-5608 TCGA-83-5908 TCGA-86-7955 TCGA-86-8074 TCGA-86-8278 TCGA-86-8280 
        1972          824          508           24          476           16 
TCGA-86-8358 TCGA-86-8585 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
          19           35          323           79          417          372 
TCGA-91-6847 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-93-8067 TCGA-95-7562 
         842          505          174           36          186         1973 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-8179 TCGA-J2-8192 TCGA-L9-A443 TCGA-MP-A4T9 
         605          964           15          154          116         1980 
TCGA-MP-A4TE TCGA-MP-A4TF 
        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          462 
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-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8508 
          66          674          216           44           29           15 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
           9            3          146          202           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-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 
        1952            1           28            5           47         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-64-1678 TCGA-64-1679 TCGA-64-1680 
        1246          910         1728         1189         1686         1126 
TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
        1968         1305          864         1559          866          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-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
         186          414          165           70          382          100 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
          77          129          214          912          467          131 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7027 
          40          164          621          305         1970         1956 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1988         1950         1963         1202          760         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
        1957         1961         1963          678         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-86-6851 TCGA-86-7701 TCGA-86-7711 
        1954         1964         1965         1959           11          630 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
         422         1968          591         1963          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8281 
        1963           13          479          489          482         1955 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          26           45           34           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-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-A4BC 
          60          310          224           35          492           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
         218          297          127           34            2          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
         377          477          476          830           84          121 
TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         553         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-97-8547 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-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
         459           44          170          114          287          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 
         238          578          435            6          266          312 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         111          102          827         1175           84         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA 
        1967         1951         1954         1954         1957         1951 
TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1944          142         1955         1971         1490          121 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                  1 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              6443               2696 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             460.5              478.0 
[1] "2.0 - 6443.0 (460.5)" "1.0 - 2696.0 (478.0)"
[1] "hr=" "1"  
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  14Q GAIN MUTATED         2       30       34        13        14         14
  14Q GAIN WILD-TYPE       3       86       98        36        56         54
                    vv
clus                 STAGE IIIB STAGE IV
  14Q GAIN MUTATED            3        5
  14Q GAIN WILD-TYPE          8       19
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 30                 86
  STAGE IB                 34                 98
  STAGE IIA                13                 36
  STAGE IIB                14                 56
  STAGE IIIA               14                 54
  STAGE IIIB                3                  8
  STAGE IV                  5                 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
  14Q GAIN MUTATED    35  66   9   5
  14Q GAIN WILD-TYPE 112 201  33  13
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               35                112
  T2               66                201
  T3                9                 33
  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    79  17    15
  14Q GAIN WILD-TYPE 222  74    59
D26V5, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                  79                222
  N1                  17                 74
  N2+N3               15                 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
  14Q GAIN MUTATED    65   5   0   0  45
  14Q GAIN WILD-TYPE 261  13   1   4  78
D26V6, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                65                261
  M1                 5                 13
  M1A                0                  1
  M1B                0                  4
  MX                45                 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"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    66  49
  14Q GAIN WILD-TYPE 189 172
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     66   49
  14Q GAIN WILD-TYPE  189  172
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               66                189
  MALE                 49                172
[1] 2 2
[1] FALSE
D26V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  14Q GAIN MUTATED                            5
  14Q GAIN WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  14Q GAIN MUTATED                                  17
  14Q GAIN WILD-TYPE                                77
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                   82
  14Q GAIN WILD-TYPE                                                221
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  14Q GAIN MUTATED                                            1
  14Q GAIN WILD-TYPE                                          4
                    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                                             3
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  14Q GAIN MUTATED                              1
  14Q GAIN WILD-TYPE                            6
D26V9, multiclass
                                                    clus
vv                                                   14Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               82
  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                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                221
  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                                        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     2 113
  14Q GAIN WILD-TYPE  19 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2  113
  14Q GAIN WILD-TYPE   19  342
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 2                 19
  YES              113                342
[1] 2 2
[1] FALSE
D26V11, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    73   5   1   7
  14Q GAIN WILD-TYPE 254   7   3  14
D26V12, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               73                254
  R1                5                  7
  R2                1                  3
  RX                7                 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 GAIN MUTATED                                  0     2
  14Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           7    93
  14Q GAIN WILD-TYPE                        28   274
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                       7                 28
  WHITE                                          93                274
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  85
  14Q GAIN WILD-TYPE   6 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   85
  14Q GAIN WILD-TYPE    6  260
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               85                260
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    21  13
  15Q GAIN WILD-TYPE 308  74
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                34                382 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                13                 74 
$`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-73-A9RS TCGA-78-7148 TCGA-78-7149 TCGA-78-7154 
          61          131          305         1944         1093         1948 
TCGA-78-7220 TCGA-78-7540 TCGA-78-8662 TCGA-86-8055 TCGA-95-7944 TCGA-97-7553 
        1965          881         1964           10          377         1332 
TCGA-97-8174 TCGA-97-8552 TCGA-MP-A4T7 TCGA-S2-AA1A 
        1965          115         1954          121 

$`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-49-AARQ 
        1700          369          890          522          354         6443 
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-50-5930 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-50-5946 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-55-1592 TCGA-55-1595 TCGA-55-1596 
        1971          424          280          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-55-6972 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-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
          18           35            6            4           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
         705           39           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-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33          462          100            6          600 
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-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
         674          216           44           23           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         1952            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
          28            5           47          162         1216         1289 
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-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
         628         1686         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-67-6217 
         573          427          385          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-69-8253 TCGA-69-8254 TCGA-69-8255 
         184           70           89          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-73-4675 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-78-7150 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-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 
        1937         1972         1949         1944          327         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-86-7713 
        1972          824         1959           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-86-8074 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         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          505          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-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        1973          568          477          476          830           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         121          553          605          964         1965         1932 
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-A4M2 TCGA-97-A4M7 TCGA-99-7458 
         147           15          148          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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
           6          266          312          111          102          827 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
        1175           84         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 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                  1 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1997               6443 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             752.5              466.5 
[1] "10.0 - 1997.0 (752.5)" "1.0 - 6443.0 (466.5)" 
[1] "hr=" "1.7"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  15Q GAIN MUTATED         2        6        6         3         5         10
  15Q GAIN WILD-TYPE       3      110      126        46        65         58
                    vv
clus                 STAGE IIIB STAGE IV
  15Q GAIN MUTATED            2        3
  15Q GAIN WILD-TYPE          9       21
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  6                110
  STAGE IB                  6                126
  STAGE IIA                 3                 46
  STAGE IIB                 5                 65
  STAGE IIIA               10                 58
  STAGE IIIB                2                  9
  STAGE IV                  3                 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     9  21   5   2
  15Q GAIN WILD-TYPE 138 246  37  16
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                9                138
  T2               21                246
  T3                5                 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    20   4    12
  15Q GAIN WILD-TYPE 281  87    62
D27V5, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                  20                281
  N1                   4                 87
  N2+N3               12                 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
  15Q GAIN MUTATED    28   2   0   1   5
  15Q GAIN WILD-TYPE 298  16   1   3 118
D27V6, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                28                298
  M1                 2                 16
  M1A                0                  1
  M1B                1                  3
  MX                 5                118
[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    17  20
  15Q GAIN WILD-TYPE 238 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     17   20
  15Q GAIN WILD-TYPE  238  201
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               17                238
  MALE                 20                201
[1] 2 2
[1] FALSE
D27V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  15Q GAIN MUTATED                            2
  15Q GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  15Q GAIN MUTATED                                   9
  15Q GAIN WILD-TYPE                                85
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                   17
  15Q GAIN WILD-TYPE                                                286
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  15Q GAIN MUTATED                                            2
  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                                             5
                    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)               17
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  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                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                286
  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                       5
  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  35
  15Q GAIN WILD-TYPE  19 420
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2   35
  15Q GAIN WILD-TYPE   19  420
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 2                 19
  YES               35                420
[1] 2 2
[1] FALSE
D27V11, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    27   2   0   1
  15Q GAIN WILD-TYPE 300  10   4  20
D27V12, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               27                300
  R1                2                 10
  R2                0                  4
  RX                1                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 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                           4    25
  15Q GAIN WILD-TYPE                        31   342
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                       4                 31
  WHITE                                          25                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  24
  15Q GAIN WILD-TYPE   7 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   24
  15Q GAIN WILD-TYPE    7  321
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               24                321
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    86  22
  16P GAIN WILD-TYPE 243  65
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               108                308 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                22                 65 
$`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          600 
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-86-7955 TCGA-86-8055 
        1950         1952         1949           11          508           10 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
         479          476          482           16           26           35 
TCGA-86-8668 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6840 TCGA-91-8496 TCGA-91-8497 
          45           10           30          372          505          174 
TCGA-93-7348 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-8177 
         127          477          121          964         1965          147 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD 
          15          115          271          427          170          287 
TCGA-J2-A4AG TCGA-L9-A443 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-S2-AA1A 
         238          116          102         1175         1967          121 

$`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-49-AARQ TCGA-50-5045 
         445          369          522          354         6443         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-50-5941 TCGA-50-5942 TCGA-50-5944 
         282          267         1091          567          883          764 
TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
         686          255         1986         1971          424          280 
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-55-6983 TCGA-55-6985 TCGA-55-6986 
        1239           25         1475         1826         1233         2151 
TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        1170           35            6           95           40          705 
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-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
           3           31           33          462          100            6 
TCGA-55-8094 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
           4           33           66          674          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-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
           9          146          202          536           48           49 
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-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 
           5           47         1216         1289         2696         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-64-5779 TCGA-64-5781 TCGA-64-5815 
        1959           62         1305          864         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-69-7761 
          31          610          427          385          141          186 
TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 
         690          165          230          184           89          100 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
          77          129          214          711          912          800 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
         131          164           38          621          519          305 
TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1970         1956         1965         1973         1988         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7155 TCGA-78-7158 
        1944         1093         1963          760         1957         1963 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
        1221          678          215         1940         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-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 
         994         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-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
         591         1963          745         1963           13           24 
TCGA-86-8076 TCGA-86-8281 TCGA-86-8358 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
         489         1955           19           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
         455          405           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-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
          35          492           36           44          218          297 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
         186           34            2         1973          568          377 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 
         476          830           84          553          605         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-97-8547 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 
        1965           87          148          197          392          459 
TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
          44          154          114          282          578          435 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 
           6          266          312          111          827           84 
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-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 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                  1 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              2370               6443 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             363.0              567.5 
[1] "3.0 - 2370.0 (363.0)" "1.0 - 6443.0 (567.5)"
[1] "hr=" "1.5"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  16P GAIN MUTATED         2       34       32        13        15         15
  16P GAIN WILD-TYPE       3       82      100        36        55         53
                    vv
clus                 STAGE IIIB STAGE IV
  16P GAIN MUTATED            2        8
  16P GAIN WILD-TYPE          9       16
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 34                 82
  STAGE IB                 32                100
  STAGE IIA                13                 36
  STAGE IIB                15                 55
  STAGE IIIA               15                 53
  STAGE IIIB                2                  9
  STAGE IV                  8                 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    43  61  13   3
  16P GAIN WILD-TYPE 104 206  29  15
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               43                104
  T2               61                206
  T3               13                 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
  16P GAIN MUTATED    74  25    18
  16P GAIN WILD-TYPE 227  66    56
D28V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                  74                227
  N1                  25                 66
  N2+N3               18                 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
  16P GAIN MUTATED    77   5   0   3  33
  16P GAIN WILD-TYPE 249  13   1   1  90
D28V6, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                77                249
  M1                 5                 13
  M1A                0                  1
  M1B                3                  1
  MX                33                 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"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    66  55
  16P GAIN WILD-TYPE 189 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     66   55
  16P GAIN WILD-TYPE  189  166
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               66                189
  MALE                 55                166
[1] 2 2
[1] FALSE
D28V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16P GAIN MUTATED                            3
  16P GAIN WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16P GAIN MUTATED                                  14
  16P GAIN WILD-TYPE                                80
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                   88
  16P GAIN WILD-TYPE                                                215
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16P GAIN MUTATED                                            2
  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                                             4
                    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)               88
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  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                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                215
  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                       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"
D28V10, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     4 117
  16P GAIN WILD-TYPE  17 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4  117
  16P GAIN WILD-TYPE   17  338
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 4                 17
  YES              117                338
[1] 2 2
[1] FALSE
D28V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    86   3   1   7
  16P GAIN WILD-TYPE 241   9   3  14
D28V12, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               86                241
  R1                3                  9
  R2                1                  3
  RX                7                 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
  16P GAIN MUTATED                                  1     2
  16P GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                           8    97
  16P GAIN WILD-TYPE                        27   270
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                       8                 27
  WHITE                                          97                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"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  94
  16P GAIN WILD-TYPE   6 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   94
  16P GAIN WILD-TYPE    6  251
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               94                251
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    65  18
  16Q GAIN WILD-TYPE 264  69
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                83                333 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                 69 
$`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          600           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-L9-A8F4 TCGA-MN-A4N4 TCGA-S2-AA1A 
         170          287          102         1175          121 

$`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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        6443         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5941 
        1499          246          282          267         1091          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 
         883          764          686          255         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
         424          280         1479         1375           87            2 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 
         993         1239           25         1475         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 
        2151         1170           18           35            6            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
          95           40          705           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-55-8090 TCGA-55-8094 TCGA-55-8096 
           5           33          462            6            4           47 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           66          674          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-55-8513 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-62-8395 TCGA-62-8397 TCGA-62-8399 
          28            5           47         1216         1289         2696 
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-64-1680 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-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         866           31          610          573          427          385 
TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
         141          186          690          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-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 
        1600          711          912          800          131          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7031 
          38          621          519          305         1970         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-78-7155 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-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
         215         1940         1934         1937         1965         1972 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 
        1949         1944          327          881          994         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-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        1959          630          422         1968          591         1963 
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-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
        1955           19           26           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
         455          405           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-91-7771 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
          35          492          505           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
         297          127          186           34            2         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
         568          377          477          476          830           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 
         121          553          605          964         1932          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-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 
         148          197          392          459           44          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-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 
           6          266          312          111          827           84 
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-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 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                  1 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              2370               6443 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               414                519 
[1] "3.0 - 2370.0 (414.0)" "1.0 - 6443.0 (519.0)"
[1] "hr=" "1.3"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  16Q GAIN MUTATED         2       25       23        11        11         14
  16Q GAIN WILD-TYPE       3       91      109        38        59         54
                    vv
clus                 STAGE IIIB STAGE IV
  16Q GAIN MUTATED            2        5
  16Q GAIN WILD-TYPE          9       19
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 25                 91
  STAGE IB                 23                109
  STAGE IIA                11                 38
  STAGE IIB                11                 59
  STAGE IIIA               14                 54
  STAGE IIIB                2                  9
  STAGE IV                  5                 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    32  46  11   3
  16Q GAIN WILD-TYPE 115 221  31  15
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               32                115
  T2               46                221
  T3               11                 31
  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    58  18    15
  16Q GAIN WILD-TYPE 243  73    59
D29V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                  58                243
  N1                  18                 73
  N2+N3               15                 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
  16Q GAIN MUTATED    64   3   0   2  23
  16Q GAIN WILD-TYPE 262  15   1   2 100
D29V6, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                64                262
  M1                 3                 15
  M1A                0                  1
  M1B                2                  2
  MX                23                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"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    48  45
  16Q GAIN WILD-TYPE 207 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     48   45
  16Q GAIN WILD-TYPE  207  176
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               48                207
  MALE                 45                176
[1] 2 2
[1] FALSE
D29V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16Q GAIN MUTATED                            2
  16Q GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16Q GAIN MUTATED                                   8
  16Q GAIN WILD-TYPE                                86
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                   67
  16Q GAIN WILD-TYPE                                                236
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16Q GAIN MUTATED                                            2
  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                                             4
                    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)               67
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  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                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  86
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                236
  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                       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"
D29V10, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     3  90
  16Q GAIN WILD-TYPE  18 365
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   90
  16Q GAIN WILD-TYPE   18  365
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 3                 18
  YES               90                365
[1] 2 2
[1] FALSE
D29V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    67   4   1   5
  16Q GAIN WILD-TYPE 260   8   3  16
D29V12, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               67                260
  R1                4                  8
  R2                1                  3
  RX                5                 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
  16Q GAIN MUTATED                                  1     2
  16Q GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                           6    73
  16Q GAIN WILD-TYPE                        29   294
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                       6                 29
  WHITE                                          73                294
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  71
  16Q GAIN WILD-TYPE   6 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   71
  16Q GAIN WILD-TYPE    6  274
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               71                274
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    53  16
  17P GAIN WILD-TYPE 276  71
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                69                347 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                16                 71 
$`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-A479 
        1492          246         1130          704         1942          486 
TCGA-49-6742 TCGA-50-5930 TCGA-50-5935 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 
         445          282          653         1479           87          993 
TCGA-55-6971 TCGA-55-7815 TCGA-55-7907 TCGA-55-7995 TCGA-55-8094 TCGA-55-8207 
          25           54           16            5            4           66 
TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 TCGA-55-8615 TCGA-55-8620 TCGA-55-A494 
         674           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-L9-A743 TCGA-MN-A4N1 
          15          115           44          116          312          827 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T9 
          84         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-44-7667 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-A47A 
         535          719          385           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-49-4501 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-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
         157         1700          369          890          522          354 
TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        6443         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 
        1499          246          267         1091         2370          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         883          764          686         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-55-1596 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-55-7281 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          705 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7910 
          39           39           34           24           19          197 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
          21            3           31           33          462          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
           6          600           26           47           15           33 
TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
          46          216           44           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-55-8616 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-A4DF TCGA-62-8395 
          48         1952            1           28           47         1216 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
        1289         2696         1445         2067         2199          910 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
        1728         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-67-3773 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-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          70           89          100           77          129          214 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 
        1600          711          912          131           38          621 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         519          305         1970         1967         1956         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1973         1988         1944         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-78-7535 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-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1981         1954         1965         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 
          11          630         1968          591         1963          745 
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-86-8668 TCGA-86-8671 
          16         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-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1940           60          310          372          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          35          492          505          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 
         218          297          127          186           34         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
         568          377          477          476          830           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         121          553          605          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-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
        1965           87          148          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         427          459          170          154          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W 
         282          238          578          435            6          266 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         111          102         1175         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        1954         1957         1951         1944         1970         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
         142         1955         1971         1490          121 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                  1 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1997               6443 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               323                505 
[1] "2.0 - 1997.0 (323.0)" "1.0 - 6443.0 (505.0)"
[1] "hr=" "1.7"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  17P GAIN MUTATED         2       16       22         9         8         13
  17P GAIN WILD-TYPE       3      100      110        40        62         55
                    vv
clus                 STAGE IIIB STAGE IV
  17P GAIN MUTATED            4        5
  17P GAIN WILD-TYPE          7       19
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 16                100
  STAGE IB                 22                110
  STAGE IIA                 9                 40
  STAGE IIB                 8                 62
  STAGE IIIA               13                 55
  STAGE IIIB                4                  7
  STAGE IV                  5                 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
  17P GAIN MUTATED    21  49   4   4
  17P GAIN WILD-TYPE 126 218  38  14
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               21                126
  T2               49                218
  T3                4                 38
  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  18    16
  17P GAIN WILD-TYPE 257  73    58
D30V5, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                  44                257
  N1                  18                 73
  N2+N3               16                 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
  17P GAIN MUTATED    57   3   0   2  17
  17P GAIN WILD-TYPE 269  15   1   2 106
D30V6, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                57                269
  M1                 3                 15
  M1A                0                  1
  M1B                2                  2
  MX                17                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"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    35  44
  17P GAIN WILD-TYPE 220 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     35   44
  17P GAIN WILD-TYPE  220  177
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               35                220
  MALE                 44                177
[1] 2 2
[1] FALSE
D30V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17P GAIN MUTATED                            2
  17P GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17P GAIN MUTATED                                  16
  17P GAIN WILD-TYPE                                78
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                   52
  17P GAIN WILD-TYPE                                                251
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17P GAIN MUTATED                                            0
  17P GAIN WILD-TYPE                                          5
                    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                                             3
                    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)               52
  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                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                251
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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                       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"
D30V10, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     6  73
  17P GAIN WILD-TYPE  15 382
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      6   73
  17P GAIN WILD-TYPE   15  382
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 6                 15
  YES               73                382
[1] 2 2
[1] FALSE
D30V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    59   0   0   6
  17P GAIN WILD-TYPE 268  12   4  15
D30V12, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               59                268
  R1                0                 12
  R2                0                  4
  RX                6                 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
  17P GAIN MUTATED                                  1     2
  17P GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           3    62
  17P GAIN WILD-TYPE                        32   305
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                       3                 32
  WHITE                                          62                305
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  58
  17P GAIN WILD-TYPE   7 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   58
  17P GAIN WILD-TYPE    7  287
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               58                287
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   125  30
  17Q GAIN WILD-TYPE 204  57
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               155                261 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                 57 
$`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-49-6745 TCGA-50-5930 
         287         1421          445          369          522          282 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-6597 
         267         2370          653          567          764         1015 
TCGA-53-7813 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6971 TCGA-55-7281 
         424         1479           87          993           25           18 
TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 
          34           54           19           16           21           31 
TCGA-55-7995 TCGA-55-8089 TCGA-55-8094 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 
           5          100            4           33           66          674 
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-95-8039 TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 TCGA-97-8175 
         377          830           84         1332          775           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-99-8025 TCGA-99-8032 
         147           15          148          115          427           44 
TCGA-99-8033 TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         170          116          312          827         1175           84 
TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE 
        1946         1954         1957         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-49-6744 TCGA-49-6761 TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         890          354         6443         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5932 TCGA-50-5942 
         785          944         1499          246         1091          883 
TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
         686          255          105         1986         1971          280 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 
         701         1178         1375            2           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-55-7283 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-55-7728 TCGA-55-7910 TCGA-55-7914 
         705           39           39           24          197            3 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 
          33          462            6          600           26           47 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
          15           46          216           44           29           11 
TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 
          15            9            3          146          536           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF 
         106           33           42            1           28           47 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
        1216         1289         2696         2067         2199          910 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
        1728         1189         1686         1126         1968           62 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 
        1305          864         1559          866          610          427 
TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
         385          141          422          186          690          414 
TCGA-69-7765 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
         165           89          100           77          129          214 
TCGA-73-4659 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-75-7025 
         711          131           38          621          305         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
        1956         1965         1988         1944         1963         1202 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 
         760         1957         1961         1963          678         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
        1950         1934         1972         1949         1944          881 
TCGA-78-8648 TCGA-78-8655 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 
        1971         1981         1965         1972          824           11 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
        1968         1963          745         1963           13          489 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 
         476           16         1955           26           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
         455          405           10           39         1940           60 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         310          372          842           35          492          505 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-95-7562 
         174           36           44          218          297         1973 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
         477          476          121          553          605          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-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SW TCGA-MP-A4T2 
           6          266          111          102         1967         1951 
TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1954         1951         1944         1970          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1971         1490          121 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                  1 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              2370               6443 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               424                505 
[1] "2.0 - 2370.0 (424.0)" "1.0 - 6443.0 (505.0)"
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  17Q GAIN MUTATED         2       36       51        19        24         30
  17Q GAIN WILD-TYPE       3       80       81        30        46         38
                    vv
clus                 STAGE IIIB STAGE IV
  17Q GAIN MUTATED            7       11
  17Q GAIN WILD-TYPE          4       13
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 36                 80
  STAGE IB                 51                 81
  STAGE IIA                19                 30
  STAGE IIB                24                 46
  STAGE IIIA               30                 38
  STAGE IIIB                7                  4
  STAGE IV                 11                 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
  17Q GAIN MUTATED    48 107  16   7
  17Q GAIN WILD-TYPE  99 160  26  11
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               48                 99
  T2              107                160
  T3               16                 26
  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   108  34    34
  17Q GAIN WILD-TYPE 193  57    40
D31V5, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                 108                193
  N1                  34                 57
  N2+N3               34                 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
  17Q GAIN MUTATED   127   9   0   2  42
  17Q GAIN WILD-TYPE 199   9   1   2  81
D31V6, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               127                199
  M1                 9                  9
  M1A                0                  1
  M1B                2                  2
  MX                42                 81
[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    96  84
  17Q GAIN WILD-TYPE 159 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     96   84
  17Q GAIN WILD-TYPE  159  137
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               96                159
  MALE                 84                137
[1] 2 2
[1] FALSE
D31V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17Q GAIN MUTATED                            6
  17Q GAIN WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17Q GAIN MUTATED                                  36
  17Q GAIN WILD-TYPE                                58
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                  121
  17Q GAIN WILD-TYPE                                                182
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17Q GAIN MUTATED                                            1
  17Q GAIN WILD-TYPE                                          4
                    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                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  17Q GAIN MUTATED                              1
  17Q GAIN WILD-TYPE                            6
D31V9, multiclass
                                                    clus
vv                                                   17Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                36
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              121
  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                                          9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  58
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                182
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  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                       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"
D31V10, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     8 172
  17Q GAIN WILD-TYPE  13 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      8  172
  17Q GAIN WILD-TYPE   13  283
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 8                 13
  YES              172                283
[1] 2 2
[1] FALSE
D31V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED   118   4   2  14
  17Q GAIN WILD-TYPE 209   8   2   7
D31V12, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0              118                209
  R1                4                  8
  R2                2                  2
  RX               14                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 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                           8   141
  17Q GAIN WILD-TYPE                        27   226
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                       8                 27
  WHITE                                         141                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"
D31V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     3 125
  17Q GAIN WILD-TYPE   4 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3  125
  17Q GAIN WILD-TYPE    4  220
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              125                220
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    64  17
  18P GAIN WILD-TYPE 265  70
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                81                335 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                17                 70 
$`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-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-97-7546 
         372           36         1973          377          477          964 
TCGA-97-7554 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-L9-A443 TCGA-L9-A444 
         775           87           15          115          116            6 
TCGA-MN-A4N4 TCGA-MP-A4TK TCGA-S2-AA1A 
        1175         1971          121 

$`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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         890          522         6443         2174         2146          455 
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-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
         653          567          883          764          686         1015 
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-55-5899 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-55-6983 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-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40          705           39           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
          54           19          197           21            3            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
          33          462            6          600           26            4 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
          15           33           46           66          674          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-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
           3          146          202          536           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-62-8395 TCGA-62-8397 TCGA-62-A46U 
        1952            1           28         1216         1289         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
        2199         1246          910         1189         1686         1126 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        1968         1959         1305         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-69-7765 TCGA-69-7974 
         422          202          186          690          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-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 
        1600          711          800          131           38          621 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         519          305         1970         1967         1956         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1973         1988         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-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
        1940         1950         1934         1937         1965         1972 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
        1944          881          994         1949         1971         1981 
TCGA-78-8660 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1954         1965         1972          824         1959           11 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8056 TCGA-86-8073 
         630         1968          591         1963         1963           13 
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-86-8668 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-91-6830 TCGA-91-6835 
          10           14           39          323           60           79 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         417          842          224           35          492          505 
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-95-7948 TCGA-95-8039 TCGA-95-8494 
          34            2          568          476          830           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         121          553          605         1965         1932         1332 
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-97-8547 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-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-A50W TCGA-L9-A743 TCGA-L9-A7SV 
         238          578          435          266          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         102          827           84         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-A5C7 
        1970         1970          142         1955         1490 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                  1 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              2696               6443 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               400                505 
[1] "5.0 - 2696.0 (400.0)" "1.0 - 6443.0 (505.0)"
[1] "hr=" "1.1"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  18P GAIN MUTATED         3       23       24        10        12         15
  18P GAIN WILD-TYPE       2       93      108        39        58         53
                    vv
clus                 STAGE IIIB STAGE IV
  18P GAIN MUTATED            2        1
  18P GAIN WILD-TYPE          9       23
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 23                 93
  STAGE IB                 24                108
  STAGE IIA                10                 39
  STAGE IIB                12                 58
  STAGE IIIA               15                 53
  STAGE IIIB                2                  9
  STAGE IV                  1                 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
  18P GAIN MUTATED    32  48   7   3
  18P GAIN WILD-TYPE 115 219  35  15
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               32                115
  T2               48                219
  T3                7                 35
  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    59  16    14
  18P GAIN WILD-TYPE 242  75    60
D32V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                  59                242
  N1                  16                 75
  N2+N3               14                 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
  18P GAIN MUTATED    66   1   0   0  23
  18P GAIN WILD-TYPE 260  17   1   4 100
D32V6, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                66                260
  M1                 1                 17
  M1A                0                  1
  M1B                0                  4
  MX                23                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"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    45  45
  18P GAIN WILD-TYPE 210 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     45   45
  18P GAIN WILD-TYPE  210  176
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               45                210
  MALE                 45                176
[1] 2 2
[1] FALSE
D32V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18P GAIN MUTATED                            4
  18P GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18P GAIN MUTATED                                  15
  18P GAIN WILD-TYPE                                79
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                   56
  18P GAIN WILD-TYPE                                                247
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18P GAIN MUTATED                                            1
  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                                             3
                    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)               56
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  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                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  79
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                247
  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                       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"
D32V10, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     3  87
  18P GAIN WILD-TYPE  18 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3   87
  18P GAIN WILD-TYPE   18  368
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 3                 18
  YES               87                368
[1] 2 2
[1] FALSE
D32V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    63   2   0   6
  18P GAIN WILD-TYPE 264  10   4  15
D32V12, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               63                264
  R1                2                 10
  R2                0                  4
  RX                6                 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 GAIN MUTATED                                  1     1
  18P GAIN WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           4    74
  18P GAIN WILD-TYPE                        31   293
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                       4                 31
  WHITE                                          74                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"
D32V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  69
  18P GAIN WILD-TYPE   7 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   69
  18P GAIN WILD-TYPE    7  276
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               69                276
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    52  10
  18Q GAIN WILD-TYPE 277  77
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                62                354 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                 77 
$`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-50-5931 TCGA-53-7813 TCGA-55-1595 TCGA-55-7907 
         466          896          267          424         1479           16 
TCGA-55-8089 TCGA-55-8096 TCGA-55-8508 TCGA-55-8511 TCGA-55-8615 TCGA-55-8620 
         100           47           15            9           15           66 
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-64-1678 TCGA-64-5779 TCGA-69-7764 TCGA-69-7973 
        1728          628         1189          864          414          230 
TCGA-69-7980 TCGA-69-8253 TCGA-71-6725 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
         382          100           61          467           40          164 
TCGA-78-7148 TCGA-78-7167 TCGA-78-7542 TCGA-86-7713 TCGA-86-7955 TCGA-86-8075 
        1944         1937         1952          422          508          479 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-A4D0 TCGA-91-6831 TCGA-91-6840 
          19           26           35           30          310          372 
TCGA-91-8499 TCGA-95-7562 TCGA-97-7546 TCGA-97-7554 TCGA-97-8175 TCGA-97-8552 
          36         1973          964          775           87          115 
TCGA-L9-A7SV TCGA-S2-AA1A 
         111          121 

$`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-49-6761 TCGA-49-AARQ 
         445          369          890          522          354         6443 
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-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         883          764          686         1015          255          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-55-6980 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          705           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-55-8090 TCGA-55-8091 TCGA-55-8092 
           5           33          462            6          600           26 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
           4           15           33           46           66          674 
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-55-8510 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-A491 TCGA-55-A492 TCGA-55-A493 TCGA-62-8395 TCGA-62-8397 TCGA-62-A46U 
        1952            1           28         1216         1289         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        2199         1246          910         1686         1126         1968 
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-67-3774 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-69-7765 TCGA-69-7974 
         422          202          186          690          165          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 
          70           89           77          129          214         1600 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 
         711          912          800          131           38          621 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         519          305         1970         1967         1956         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1973         1988         1950         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-78-7220 
         678          215         1940         1950         1934         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-86-7714 
        1972          824         1959           11          630         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-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
          24          489          476          482           16         1955 
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-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
          79          417          842          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         505          174           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-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
         476          830           84          121          553          605 
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-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M2 
         182         1965          147           15          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-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-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 
         435          116            6          266          312          102 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         827         1175           84         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 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                  1 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              2696               6443 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             418.0              487.5 
[1] "5.0 - 2696.0 (418.0)" "1.0 - 6443.0 (487.5)"
[1] "hr=" "1.1"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  18Q GAIN MUTATED         2       14       19         8         7         11
  18Q GAIN WILD-TYPE       3      102      113        41        63         57
                    vv
clus                 STAGE IIIB STAGE IV
  18Q GAIN MUTATED            2        3
  18Q GAIN WILD-TYPE          9       21
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 14                102
  STAGE IB                 19                113
  STAGE IIA                 8                 41
  STAGE IIB                 7                 63
  STAGE IIIA               11                 57
  STAGE IIIB                2                  9
  STAGE IV                  3                 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
  18Q GAIN MUTATED    19  40   5   2
  18Q GAIN WILD-TYPE 128 227  37  16
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               19                128
  T2               40                227
  T3                5                 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
  18Q GAIN MUTATED    43  12    11
  18Q GAIN WILD-TYPE 258  79    63
D33V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                  43                258
  N1                  12                 79
  N2+N3               11                 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
  18Q GAIN MUTATED    45   2   0   1  18
  18Q GAIN WILD-TYPE 281  16   1   3 105
D33V6, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                45                281
  M1                 2                 16
  M1A                0                  1
  M1B                1                  3
  MX                18                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"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    32  34
  18Q GAIN WILD-TYPE 223 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     32   34
  18Q GAIN WILD-TYPE  223  187
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               32                223
  MALE                 34                187
[1] 2 2
[1] FALSE
D33V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18Q GAIN MUTATED                            2
  18Q GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18Q GAIN MUTATED                                  10
  18Q GAIN WILD-TYPE                                84
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                   41
  18Q GAIN WILD-TYPE                                                262
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18Q GAIN MUTATED                                            1
  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                                             3
                    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)               41
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  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                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  84
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                262
  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                       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"
D33V10, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  64
  18Q GAIN WILD-TYPE  19 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   64
  18Q GAIN WILD-TYPE   19  391
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 2                 19
  YES               64                391
[1] 2 2
[1] FALSE
D33V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    41   1   0   7
  18Q GAIN WILD-TYPE 286  11   4  14
D33V12, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               41                286
  R1                1                 11
  R2                0                  4
  RX                7                 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
  18Q GAIN MUTATED                                  1     2
  18Q GAIN WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           7    51
  18Q GAIN WILD-TYPE                        28   316
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                       7                 28
  WHITE                                          51                316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  55
  18Q GAIN WILD-TYPE   7 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   55
  18Q GAIN WILD-TYPE    7  290
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               55                290
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    27   2
  19P GAIN WILD-TYPE 302  85
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                29                387 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 85 
$`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-95-8494 TCGA-97-7554 TCGA-97-7937 
          26           35          377           84          775          181 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-MN-A4N4 TCGA-S2-AA1A 
         182           87           15         1175          121 

$`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-49-AARQ 
         445          369          890          522          354         6443 
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-50-5931 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-50-7109 TCGA-50-8460 
         883          764          686         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-55-6642 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-55-7573 
        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          705           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          24           54           19          197           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33          462          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
         600           26            4           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          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-55-8616 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-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
           1           28            5           47          162         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        1289         1970         1445         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-67-3770 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-69-7979 TCGA-69-7980 
         414          165          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-73-4676 TCGA-73-4677 
         912          800          467          131          164           38 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
         621          519          305         1970         1967         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        1965         1973         1988         1950         1944         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-78-7159 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-86-7713 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-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
         479          489          476          482           16         1955 
TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          19           45           34           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-91-6836 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          505          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-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 
          34            2         1973          568          477          476 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
         830          121          553          605          964         1965 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8177 
        1932         1332           22          107         1965          147 
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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 
         266          312          111          102          827           84 
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-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 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                15                  1 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              2696               6443 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               337                479 
[1] "15.0 - 2696.0 (337.0)" "1.0 - 6443.0 (479.0)" 
[1] "hr=" "4.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  19P GAIN MUTATED         0        8        8         2         4          7
  19P GAIN WILD-TYPE       5      108      124        47        66         61
                    vv
clus                 STAGE IIIB STAGE IV
  19P GAIN MUTATED            0        2
  19P GAIN WILD-TYPE         11       22
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                  8                108
  STAGE IB                  8                124
  STAGE IIA                 2                 47
  STAGE IIB                 4                 66
  STAGE IIIA                7                 61
  STAGE IIIB                0                 11
  STAGE IV                  2                 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
  19P GAIN MUTATED     9  16   6   0
  19P GAIN WILD-TYPE 138 251  36  18
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                9                138
  T2               16                251
  T3                6                 36
  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    17   7     6
  19P GAIN WILD-TYPE 284  84    68
D34V5, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                  17                284
  N1                   7                 84
  N2+N3                6                 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
  19P GAIN MUTATED    24   1   0   1   5
  19P GAIN WILD-TYPE 302  17   1   3 118
D34V6, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                24                302
  M1                 1                 17
  M1A                0                  1
  M1B                1                  3
  MX                 5                118
[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    14  17
  19P GAIN WILD-TYPE 241 204
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     14   17
  19P GAIN WILD-TYPE  241  204
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               14                241
  MALE                 17                204
[1] 2 2
[1] FALSE
D34V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19P GAIN MUTATED                            2
  19P GAIN WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19P GAIN MUTATED                                   4
  19P GAIN WILD-TYPE                                90
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                   18
  19P GAIN WILD-TYPE                                                285
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19P GAIN MUTATED                                            1
  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                                             3
                    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)               18
  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                                     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                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                285
  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                       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"
D34V10, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  30
  19P GAIN WILD-TYPE  20 425
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   30
  19P GAIN WILD-TYPE   20  425
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 1                 20
  YES               30                425
[1] 2 2
[1] FALSE
D34V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    18   1   0   1
  19P GAIN WILD-TYPE 309  11   4  20
D34V12, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               18                309
  R1                1                 11
  R2                0                  4
  RX                1                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 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                           3    25
  19P GAIN WILD-TYPE                        32   342
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                       3                 32
  WHITE                                          25                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  26
  19P GAIN WILD-TYPE   6 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   26
  19P GAIN WILD-TYPE    6  319
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               26                319
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    53  10
  19Q GAIN WILD-TYPE 276  77
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                63                353 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                 77 
$`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-86-8075 
          40         1963         1948          422           10          479 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8673 TCGA-91-6830 TCGA-95-7043 
          19           26           35          455           60            2 
TCGA-95-7944 TCGA-95-A4VP TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 
         377          605          775          181          182         1965 
TCGA-97-8179 TCGA-99-8025 TCGA-L9-A443 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4T7 
          15          427          116          102         1175         1954 
TCGA-MP-A4TC TCGA-MP-A4TH TCGA-S2-AA1A 
        1944          142          121 

$`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-49-AARQ TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
         354         6443         2174          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-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
         255          105         1971          424          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-55-6972 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          705           39           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          24           54           19          197           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33          462          100            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
         600            4           47           15           33           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
          66          674          216           44           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-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         202           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-62-8402 
          47          162         1216         1289         1970         1445 
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-64-5774 TCGA-64-5775 
        1189         1686         1126         1968         1959           62 
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-67-6217 TCGA-69-7760 TCGA-69-7761 
         385          174          141          422          202          186 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 TCGA-69-8255 
         165          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-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         467          131          164           38          621          519 
TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         305         1970         1967         1956         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
        1988         1950         1944         1093         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-86-7714 
        1972          824         1959           11          630         1968 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
         591         1963          508          745         1963           13 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
          24          489          476          482           16         1955 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
          45           34           18           15          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 
          30           14           39          323         1940          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          505          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
         297          127          186           34         1973          568 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
         477          476          830           84          121          553 
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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV 
         266          312          111          827           84         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-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1970         1955         1971         1490 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                  1 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              2696               6443 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               414                492 
[1] "2.0 - 2696.0 (414.0)" "1.0 - 6443.0 (492.0)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  19Q GAIN MUTATED         1       17       22         7         6         14
  19Q GAIN WILD-TYPE       4       99      110        42        64         54
                    vv
clus                 STAGE IIIB STAGE IV
  19Q GAIN MUTATED            0        4
  19Q GAIN WILD-TYPE         11       20
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 17                 99
  STAGE IB                 22                110
  STAGE IIA                 7                 42
  STAGE IIB                 6                 64
  STAGE IIIA               14                 54
  STAGE IIIB                0                 11
  STAGE IV                  4                 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    22  38  10   0
  19Q GAIN WILD-TYPE 125 229  32  18
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               22                125
  T2               38                229
  T3               10                 32
  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    45  11    14
  19Q GAIN WILD-TYPE 256  80    60
D35V5, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                  45                256
  N1                  11                 80
  N2+N3               14                 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    49   2   0   2  18
  19Q GAIN WILD-TYPE 277  16   1   2 105
D35V6, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                49                277
  M1                 2                 16
  M1A                0                  1
  M1B                2                  2
  MX                18                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"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    30  41
  19Q GAIN WILD-TYPE 225 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     30   41
  19Q GAIN WILD-TYPE  225  180
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               30                225
  MALE                 41                180
[1] 2 2
[1] FALSE
D35V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19Q GAIN MUTATED                            4
  19Q GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19Q GAIN MUTATED                                   9
  19Q GAIN WILD-TYPE                                85
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                   46
  19Q GAIN WILD-TYPE                                                257
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19Q GAIN MUTATED                                            1
  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                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  19Q GAIN MUTATED                              1
  19Q GAIN WILD-TYPE                            6
D35V9, multiclass
                                                    clus
vv                                                   19Q GAIN MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 9
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               46
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  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                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                257
  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                       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"
D35V10, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  70
  19Q GAIN WILD-TYPE  20 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   70
  19Q GAIN WILD-TYPE   20  385
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 1                 20
  YES               70                385
[1] 2 2
[1] FALSE
D35V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    44   2   0   3
  19Q GAIN WILD-TYPE 283  10   4  18
D35V12, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               44                283
  R1                2                 10
  R2                0                  4
  RX                3                 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
  19Q GAIN MUTATED                                  0     0
  19Q GAIN WILD-TYPE                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           8    56
  19Q GAIN WILD-TYPE                        27   311
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                       8                 27
  WHITE                                          56                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"
D35V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2  55
  19Q GAIN WILD-TYPE   5 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   55
  19Q GAIN WILD-TYPE    5  290
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               55                290
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   111  32
  20P GAIN WILD-TYPE 218  55
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               143                273 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                32                 55 
$`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-44-5644 TCGA-44-5645 TCGA-44-6144 
         354          448          400          863          383          723 
TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 
         845          658          705         1864          592          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
         557         1970          535          719           99          486 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 TCGA-49-4506 
         287          337          415           76         1081          999 
TCGA-49-4510 TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 
         896         2174         2146          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-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6972 
        1375           87            2          993         1239         1475 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7724 TCGA-55-7726 TCGA-55-7995 TCGA-55-8085 
         121           95          705           39            5           33 
TCGA-55-8087 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 
         462           47           15           33           46          674 
TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 
          23            8           15            3          202          536 
TCGA-55-8615 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          15           29         1952           28            5           47 
TCGA-55-A4DG TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 TCGA-64-5775 TCGA-67-3771 
         162         2696         1445          628           62          610 
TCGA-67-3772 TCGA-69-7763 TCGA-69-7764 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         573          690          414           70           89          382 
TCGA-69-8253 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4677 
         100           61         1600          912          467           38 
TCGA-73-A9RS TCGA-75-7027 TCGA-75-7031 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
         305         1956         1965          760         1948         1957 
TCGA-78-7159 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7542 
        1221         1950         1937         1965         1949         1952 
TCGA-78-8640 TCGA-83-5908 TCGA-86-7713 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 
        1949          824          422          745           10           13 
TCGA-86-8075 TCGA-86-8585 TCGA-86-8669 TCGA-91-6829 TCGA-91-6836 TCGA-91-6840 
         479           35           34         1940          417          372 
TCGA-91-6847 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7567 TCGA-95-8494 
         842           36           44          186          568           84 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 
         964         1332          181         1965           87           15 
TCGA-97-8552 TCGA-99-8025 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T2 
         115          427          102          827           84         1951 
TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK TCGA-S2-AA1A 
        1954         1970         1970         1971          121 

$`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-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1130         1163         1036          190          722         1013 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 
         328          302          704         1938         1942         1978 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7670 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A 
         444          366          882          385          260          466 
TCGA-44-A47G TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 
         351         1932         1421          428          268          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-49-AARQ TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
        6443          455          785          246          282         1091 
TCGA-50-5933 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 
        2370          883          764         1015          105         1986 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-6712 TCGA-55-6971 
        1971          280         1178         1479           24           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-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 
          35            6            4           40           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-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
           3           31          100            6          600           26 
TCGA-55-8094 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
           4           66          216           44           29           11 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
         228            9          146           48           49           66 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-62-8395 
         106           33           42           48            1         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-64-1681 TCGA-64-5774 
        1728         1189         1686         1126         1968         1959 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 
        1305          864         1559          866           31          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-69-7973 TCGA-69-7974 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
         165          230          184           77          129          214 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 
         711          800          131           40          164          621 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
         519         1970         1967         1973         1988         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 
        1944         1093         1963         1202         1961         1963 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7535 TCGA-78-7537 
         678          215         1940         1934         1972         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
         327          881          994         1971         1981         1954 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
        1964         1965         1972         1959           11          630 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8074 
        1968          591         1963          508         1963           24 
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-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-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
         310           79          224           35          492          505 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 
         174          218          297          127           34            2 
TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
        1973          377          477          476          830          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 
         553          605         1965         1932          775           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 
         107          182          147          148          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-A443 
         287          282          238          578          435          116 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV 
           6          266          312          111         1175         1946 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1967         1954         1957         1980         1951         1944 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
         142         1955         1490 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                  1 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              2696               6443 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               536                455 
[1] "2.0 - 2696.0 (536.0)" "1.0 - 6443.0 (455.0)"
[1] "hr=" "1.4"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  20P GAIN MUTATED         3       42       52        13        23         19
  20P GAIN WILD-TYPE       2       74       80        36        47         49
                    vv
clus                 STAGE IIIB STAGE IV
  20P GAIN MUTATED            3        6
  20P GAIN WILD-TYPE          8       18
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 42                 74
  STAGE IB                 52                 80
  STAGE IIA                13                 36
  STAGE IIB                23                 47
  STAGE IIIA               19                 49
  STAGE IIIB                3                  8
  STAGE IV                  6                 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
  20P GAIN MUTATED    49  96  13   3
  20P GAIN WILD-TYPE  98 171  29  15
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               49                 98
  T2               96                171
  T3               13                 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   110  26    20
  20P GAIN WILD-TYPE 191  65    54
D36V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                 110                191
  N1                  26                 65
  N2+N3               20                 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
  20P GAIN MUTATED   102   4   0   2  50
  20P GAIN WILD-TYPE 224  14   1   2  73
D36V6, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               102                224
  M1                 4                 14
  M1A                0                  1
  M1B                2                  2
  MX                50                 73
[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    85  76
  20P GAIN WILD-TYPE 170 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     85   76
  20P GAIN WILD-TYPE  170  145
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               85                170
  MALE                 76                145
[1] 2 2
[1] FALSE
D36V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20P GAIN MUTATED                            4
  20P GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20P GAIN MUTATED                                  21
  20P GAIN WILD-TYPE                                73
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                  115
  20P GAIN WILD-TYPE                                                188
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20P GAIN MUTATED                                            2
  20P GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20P GAIN MUTATED                                               7
  20P GAIN WILD-TYPE                                            12
                    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                                             3
                    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)              115
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     7
  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                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                188
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      12
  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                       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"
D36V10, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     7 154
  20P GAIN WILD-TYPE  14 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7  154
  20P GAIN WILD-TYPE   14  301
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 7                 14
  YES              154                301
[1] 2 2
[1] FALSE
D36V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED    98   6   2   5
  20P GAIN WILD-TYPE 229   6   2  16
D36V12, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               98                229
  R1                6                  6
  R2                2                  2
  RX                5                 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 GAIN MUTATED                                  1     3
  20P GAIN WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          18   121
  20P GAIN WILD-TYPE                        17   246
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                      18                 17
  WHITE                                         121                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"
D36V14, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     1 122
  20P GAIN WILD-TYPE   6 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      1  122
  20P GAIN WILD-TYPE    6  223
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO              122                223
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   129  36
  20Q GAIN WILD-TYPE 200  51
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               165                251 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                36                 51 
$`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-44-5645 TCGA-44-6144 
         864          354          448          400          383          723 
TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 
         845          658          705         1864          592          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-A47F TCGA-44-A4SU TCGA-49-4494 TCGA-49-4506 
          99          486          337           76         1081          999 
TCGA-49-4510 TCGA-49-4512 TCGA-49-AARQ TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 
         896          157         6443          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          705           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-55-8208 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 
         674           23           11            8           15            3 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 
         202          536           15           66           29         1952 
TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 
          28           47          162         2696         1445          628 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 
        1968         1959           62         1559          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-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
         129           61         1600          800          467          131 
TCGA-73-4677 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7153 
          38          305         1970         1956         1965          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
        1948         1957         1221         1950         1937         1965 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 
        1972         1949         1952         1949         1954          824 
TCGA-86-7713 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 
         422          508          745           10           13          479 
TCGA-86-8279 TCGA-86-8585 TCGA-86-8669 TCGA-91-6829 TCGA-91-6835 TCGA-91-6836 
         482           35           34         1940           79          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 
         372          842          492           36           44          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-8494 
          34            2         1973          568          477           84 
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-L9-A8F4 TCGA-MN-A4N1 
         115          427          578            6          102          827 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TE 
        1175           84         1946         1951         1954         1970 
TCGA-MP-A4TF TCGA-MP-A4TK TCGA-S2-AA1A 
        1970         1971          121 

$`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-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
        1163         1036          190          722         1013          863 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 
         328          302          704         1938         1942         1978 
TCGA-44-7659 TCGA-44-7661 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
         444          366          260          466          287          351 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4514 
         415         1932         1421          428          268         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-50-5072 TCGA-50-5930 TCGA-50-5932 
        2146          455          785          246          282         1091 
TCGA-50-5933 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 
        2370          883          764         1015          105         1986 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6971 TCGA-55-6980 
        1971          280         1479           87           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-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 
           6            4           95           40           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
          24           54           19           21            3           31 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 
         462          100            6          600            4           15 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 
          66          216           44           29          228            9 
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-86-8056 
          11          630         1968          591         1963         1963 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
          24          489          476           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-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
          10           30           14           39          323           60 
TCGA-91-6831 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
         310          224           35          505          174          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7944 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
         297          127          377          476          830          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7941 
         553          605         1965         1932          775           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8547 TCGA-97-A4M2 TCGA-97-A4M7 
         107          182         1965          148          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-A4E6 TCGA-L9-A443 TCGA-L9-A50W 
         287          282          238          435          116          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
         312          111         1967         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1951         1944          142         1955         1490 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                  1 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              6443               2370 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               508                455 
[1] "2.0 - 6443.0 (508.0)" "1.0 - 2370.0 (455.0)"
[1] "hr=" "1.4"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  20Q GAIN MUTATED         5       44       54        19        31         23
  20Q GAIN WILD-TYPE       0       72       78        30        39         45
                    vv
clus                 STAGE IIIB STAGE IV
  20Q GAIN MUTATED            3        7
  20Q GAIN WILD-TYPE          8       17
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   5                  0
  STAGE IA                 44                 72
  STAGE IB                 54                 78
  STAGE IIA                19                 30
  STAGE IIB                31                 39
  STAGE IIIA               23                 45
  STAGE IIIB                3                  8
  STAGE IV                  7                 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    56 109  17   3
  20Q GAIN WILD-TYPE  91 158  25  15
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               56                 91
  T2              109                158
  T3               17                 25
  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   124  35    23
  20Q GAIN WILD-TYPE 177  56    51
D37V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                 124                177
  N1                  35                 56
  N2+N3               23                 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
  20Q GAIN MUTATED   120   5   0   2  57
  20Q GAIN WILD-TYPE 206  13   1   2  66
D37V6, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               120                206
  M1                 5                 13
  M1A                0                  1
  M1B                2                  2
  MX                57                 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"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    95  91
  20Q GAIN WILD-TYPE 160 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     95   91
  20Q GAIN WILD-TYPE  160  130
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               95                160
  MALE                 91                130
[1] 2 2
[1] FALSE
D37V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20Q GAIN MUTATED                            4
  20Q GAIN WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20Q GAIN MUTATED                                  28
  20Q GAIN WILD-TYPE                                66
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                  132
  20Q GAIN WILD-TYPE                                                171
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20Q GAIN MUTATED                                            2
  20Q GAIN WILD-TYPE                                          3
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20Q GAIN MUTATED                                               7
  20Q GAIN WILD-TYPE                                            12
                    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                                             2
                    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)              132
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     7
  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                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                171
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      12
  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"
D37V10, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     5 181
  20Q GAIN WILD-TYPE  16 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5  181
  20Q GAIN WILD-TYPE   16  274
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 5                 16
  YES              181                274
[1] 2 2
[1] FALSE
D37V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   119   5   2   7
  20Q GAIN WILD-TYPE 208   7   2  14
D37V12, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              119                208
  R1                5                  7
  R2                2                  2
  RX                7                 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                          19   139
  20Q GAIN WILD-TYPE                        16   228
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                      19                 16
  WHITE                                         139                228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3 137
  20Q GAIN WILD-TYPE   4 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  137
  20Q GAIN WILD-TYPE    4  208
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              137                208
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    54  19
  21Q GAIN WILD-TYPE 275  68
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                73                343 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                 68 
$`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-55-8208 TCGA-55-8511 TCGA-55-8615 TCGA-55-A48Z TCGA-62-8398 
          66          674            9           15           29         1970 
TCGA-62-8399 TCGA-64-1678 TCGA-64-1680 TCGA-67-3771 TCGA-67-6217 TCGA-69-8253 
        2696         1189         1126          610          422          100 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4677 TCGA-73-7499 TCGA-75-6214 TCGA-78-7147 
         214           61           38          519         1970         1950 
TCGA-78-7155 TCGA-78-7163 TCGA-78-7535 TCGA-78-7539 TCGA-78-7542 TCGA-78-8662 
        1957         1950         1972          327         1952         1964 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-91-8496 TCGA-91-8499 TCGA-95-7944 
         479          482           19          505           36          377 
TCGA-97-7546 TCGA-97-7553 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-J2-A4AD 
         964         1332          147           15          115          287 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC 
           6          827           84         1954         1951         1944 
TCGA-S2-AA1A 
         121 

$`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-49-AARQ TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        6443         2174          455          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 
         246          282         1091         2370          653          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
         764          686          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-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 
          24         1239           25         1475         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          705           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-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33          462          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
         600           26            4           47           15           33 
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-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
          15          228            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-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
          48         1952            1           28            5           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
         162         1216         1289         1445         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-64-5774 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-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
          31          573          427          385          174          141 
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-69-8254 TCGA-69-8255 
         184           70           89          382           77          129 
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-73-7498 TCGA-73-A9RS TCGA-75-7025 TCGA-75-7027 
          40          164          621          305         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-78-7156 TCGA-78-7158 TCGA-78-7159 
        1202          760         1948         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-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1949         1944          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-86-7953 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-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 
         489          476           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-91-6829 
          10           30           14           39          323         1940 
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-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
         224           35          492          174           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
         297          127          186           34            2         1973 
TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
         568          477          476          830           84          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 
         553          605         1965         1932          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-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-L9-A443 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
         435          116          266          312          111          102 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 
        1175         1946         1967         1951         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 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                  1 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              2696               6443 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               519                459 
[1] "3.0 - 2696.0 (519.0)" "1.0 - 6443.0 (459.0)"
[1] "hr=" "1.1"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  21Q GAIN MUTATED         1       21       26        10         8         15
  21Q GAIN WILD-TYPE       4       95      106        39        62         53
                    vv
clus                 STAGE IIIB STAGE IV
  21Q GAIN MUTATED            3        3
  21Q GAIN WILD-TYPE          8       21
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 21                 95
  STAGE IB                 26                106
  STAGE IIA                10                 39
  STAGE IIB                 8                 62
  STAGE IIIA               15                 53
  STAGE IIIB                3                  8
  STAGE IV                  3                 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
  21Q GAIN MUTATED    30  49   6   2
  21Q GAIN WILD-TYPE 117 218  36  16
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               30                117
  T2               49                218
  T3                6                 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
  21Q GAIN MUTATED    49  14    20
  21Q GAIN WILD-TYPE 252  77    54
D38V5, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                  49                252
  N1                  14                 77
  N2+N3               20                 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
  21Q GAIN MUTATED    61   3   0   0  22
  21Q GAIN WILD-TYPE 265  15   1   4 101
D38V6, multiclass
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                61                265
  M1                 3                 15
  M1A                0                  1
  M1B                0                  4
  MX                22                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"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    55  32
  21Q GAIN WILD-TYPE 200 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     55   32
  21Q GAIN WILD-TYPE  200  189
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               55                200
  MALE                 32                189
[1] 2 2
[1] FALSE
D38V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  21Q GAIN MUTATED                            3
  21Q GAIN WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  21Q GAIN MUTATED                                  15
  21Q GAIN WILD-TYPE                                79
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                   57
  21Q GAIN WILD-TYPE                                                246
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  21Q GAIN MUTATED                                            1
  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                                             4
                    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)               57
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  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                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  79
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                246
  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                       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"
D38V10, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4  83
  21Q GAIN WILD-TYPE  17 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4   83
  21Q GAIN WILD-TYPE   17  372
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 4                 17
  YES               83                372
[1] 2 2
[1] FALSE
D38V11, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    64   2   0   4
  21Q GAIN WILD-TYPE 263  10   4  17
D38V12, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               64                263
  R1                2                 10
  R2                0                  4
  RX                4                 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
  21Q GAIN MUTATED                                  0     2
  21Q GAIN WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           6    67
  21Q GAIN WILD-TYPE                        29   300
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                       6                 29
  WHITE                                          67                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"
D38V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  62
  21Q GAIN WILD-TYPE   6 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   62
  21Q GAIN WILD-TYPE    6  283
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               62                283
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    36  13
  22Q GAIN WILD-TYPE 293  74
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                49                367 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                13                 74 
$`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-55-8208 
         705           39           16          600           47          674 
TCGA-55-8506 TCGA-55-8514 TCGA-55-8614 TCGA-55-A491 TCGA-62-8397 TCGA-62-8398 
          11          202          536         1952         1289         1970 
TCGA-62-8402 TCGA-67-3770 TCGA-67-3771 TCGA-73-4675 TCGA-78-7150 TCGA-78-7154 
        1445           31          610           40         1963         1948 
TCGA-78-8662 TCGA-86-7713 TCGA-86-8055 TCGA-86-8073 TCGA-86-8280 TCGA-91-6847 
        1964          422           10           13           16          842 
TCGA-95-7944 TCGA-97-8174 TCGA-97-8552 TCGA-99-8033 TCGA-J2-A4AE TCGA-MP-A4SW 
         377         1965          115          170          282         1967 
TCGA-MP-A4T7 
        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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        6443         2174         2146          455          785          944 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        1499          246          282         1091         2370          653 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
         567          883          686         1015          255          105 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
        1986         1971          424          280         1178         1479 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
          87            2          993         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-55-7284 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-55-7903 TCGA-55-7910 
          39           34           24           54           19          197 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          21            3           31            5           33          462 
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-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          46           66          216           44           23           29 
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-55-8615 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-A492 TCGA-55-A493 TCGA-55-A494 
          42           29           48            1           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V 
          47          162         1216         2696         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-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
        1559          866          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-69-8253 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-73-4670 TCGA-73-4676 
         711          912          800          467          131          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 
          38          621          519          305         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-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1954         1965         1972          824         1959           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-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        1963           24          479          489          476          482 
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-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-91-6848 TCGA-91-6849 TCGA-91-7771 
          79          417          372          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
         505          174           36           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
         127          186           34            2         1973          568 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
         477          476          830           84          121          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         605          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-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
          15          148          197          271          392          427 
TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG 
         459           44          154          114          287          238 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 
         578          435          116            6          266          312 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         111          102          827         1175           84         1946 
TCGA-MP-A4T2 TCGA-MP-A4T4 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-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1970          142         1955         1971         1490 
TCGA-S2-AA1A 
         121 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                10                  1 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1978               6443 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               600                467 
[1] "10.0 - 1978.0 (600.0)" "1.0 - 6443.0 (467.0)" 
[1] "hr=" "1.3"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  22Q GAIN MUTATED         1       11       19         9         9          9
  22Q GAIN WILD-TYPE       4      105      113        40        61         59
                    vv
clus                 STAGE IIIB STAGE IV
  22Q GAIN MUTATED            0        3
  22Q GAIN WILD-TYPE         11       21
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 11                105
  STAGE IB                 19                113
  STAGE IIA                 9                 40
  STAGE IIB                 9                 61
  STAGE IIIA                9                 59
  STAGE IIIB                0                 11
  STAGE IV                  3                 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
  22Q GAIN MUTATED    14  39   6   1
  22Q GAIN WILD-TYPE 133 228  36  17
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               14                133
  T2               39                228
  T3                6                 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
  22Q GAIN MUTATED    36  15     8
  22Q GAIN WILD-TYPE 265  76    66
D39V5, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                  36                265
  N1                  15                 76
  N2+N3                8                 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
  22Q GAIN MUTATED    38   3   0   0  20
  22Q GAIN WILD-TYPE 288  15   1   4 103
D39V6, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                38                288
  M1                 3                 15
  M1A                0                  1
  M1B                0                  4
  MX                20                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"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    38  23
  22Q GAIN WILD-TYPE 217 198
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     38   23
  22Q GAIN WILD-TYPE  217  198
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               38                217
  MALE                 23                198
[1] 2 2
[1] FALSE
D39V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  22Q GAIN MUTATED                            1
  22Q GAIN WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  22Q GAIN MUTATED                                   7
  22Q GAIN WILD-TYPE                                87
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                   46
  22Q GAIN WILD-TYPE                                                257
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  22Q GAIN MUTATED                                            0
  22Q GAIN WILD-TYPE                                          5
                    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                                             5
                    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)               46
  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                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                257
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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                       5
  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  60
  22Q GAIN WILD-TYPE  20 395
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   60
  22Q GAIN WILD-TYPE   20  395
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 1                 20
  YES               60                395
[1] 2 2
[1] FALSE
D39V11, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    44   0   1   2
  22Q GAIN WILD-TYPE 283  12   3  19
D39V12, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               44                283
  R1                0                 12
  R2                1                  3
  RX                2                 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
  22Q GAIN MUTATED                                  0     1
  22Q GAIN WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           3    49
  22Q GAIN WILD-TYPE                        32   318
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                 32
  WHITE                                          49                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"
D39V14, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     1  43
  22Q GAIN WILD-TYPE   6 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   43
  22Q GAIN WILD-TYPE    6  302
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               43                302
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    49  11
  XQ GAIN WILD-TYPE 280  76
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               60               356 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               11                76 
$`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-49-AARQ 
        1864          385          466           76          354         6443 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-7109 TCGA-53-7626 TCGA-55-5899 
        2370          567          686          255         1971           87 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6987 TCGA-55-7281 TCGA-55-7726 TCGA-55-7907 
           2           24         1170           18           39           16 
TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8094 TCGA-55-8096 TCGA-55-A494 
         197           31            5            4           47            5 
TCGA-64-1676 TCGA-64-1680 TCGA-64-5775 TCGA-67-6215 TCGA-69-7980 TCGA-71-6725 
        1728         1126           62          174          382           61 
TCGA-73-4676 TCGA-73-4677 TCGA-75-7025 TCGA-75-7031 TCGA-78-7149 TCGA-78-7154 
         164           38         1967         1965         1093         1948 
TCGA-78-7155 TCGA-78-7163 TCGA-78-7535 TCGA-78-7539 TCGA-78-8640 TCGA-86-8055 
        1957         1950         1972          327         1949           10 
TCGA-86-8075 TCGA-86-8358 TCGA-86-A4P7 TCGA-91-8499 TCGA-95-7043 TCGA-97-7554 
         479           19           14           36            2          775 
TCGA-97-7937 TCGA-97-8179 TCGA-L9-A7SV TCGA-MP-A4T4 TCGA-MP-A4TI TCGA-S2-AA1A 
         181           15          111         1954         1955          121 

$`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-50-8460 TCGA-53-7624 
         653          883          764         1015          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-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
         993         1239           25         1475           67         1826 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
        1233         2151           35          121            6            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
          95           40          705           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 
          54           19           21            3           33          462 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 TCGA-55-8205 
         100            6          600           26           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          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-73-A9RS 
         467          131           40          621          519          305 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1970         1956         1973         1988         1950         1944 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
        1963         1202          760         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-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
        1949         1944          881         1952          994         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-86-8056 TCGA-86-8073 TCGA-86-8074 
        1963          508          745         1963           13           24 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8359 
         489          476          482           16         1955           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          35           45           34           18           15          455 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
         405           10           30           39          323         1940 
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-A4BC 
         224           35          492          505          174           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 
         218          297          127          186           34         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
         568          377          477          476          830           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         121          553          605          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-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
           6          266          312          102          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T8 
          84         1946         1967         1951         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-A4TK TCGA-MP-A5C7 
        1971         1490 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                 1 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             6443              2696 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            295.5             498.5 
[1] "2.0 - 6443.0 (295.5)" "1.0 - 2696.0 (498.5)"
[1] "hr=" "1.3"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  XQ GAIN MUTATED         3       17       19        10         7          8
  XQ GAIN WILD-TYPE       2       99      113        39        63         60
                   vv
clus                STAGE IIIB STAGE IV
  XQ GAIN MUTATED            2        6
  XQ GAIN WILD-TYPE          9       18
D40V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                17                99
  STAGE IB                19               113
  STAGE IIA               10                39
  STAGE IIB                7                63
  STAGE IIIA               8                60
  STAGE IIIB               2                 9
  STAGE IV                 6                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    21  41   5   4
  XQ GAIN WILD-TYPE 126 226  37  14
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              21               126
  T2              41               226
  T3               5                37
  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    45  15    11
  XQ GAIN WILD-TYPE 256  76    63
D40V5, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0                 45               256
  N1                 15                76
  N2+N3              11                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 GAIN MUTATED    46   4   0   2  19
  XQ GAIN WILD-TYPE 280  14   1   2 104
D40V6, multiclass
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               46               280
  M1                4                14
  M1A               0                 1
  M1B               2                 2
  MX               19               104
[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    35  37
  XQ GAIN WILD-TYPE 220 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     35   37
  XQ GAIN WILD-TYPE  220  184
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              35               220
  MALE                37               184
[1] 2 2
[1] FALSE
D40V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XQ GAIN MUTATED                            1
  XQ GAIN WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XQ GAIN MUTATED                                   9
  XQ GAIN WILD-TYPE                                85
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                   56
  XQ GAIN WILD-TYPE                                                247
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  XQ GAIN MUTATED                                            2
  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                                             5
                   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)              56
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                       2
  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                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               247
  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                      5
  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  69
  XQ GAIN WILD-TYPE  18 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   69
  XQ GAIN WILD-TYPE   18  386
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                3                18
  YES              69               386
[1] 2 2
[1] FALSE
D40V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    50   2   1   2
  XQ GAIN WILD-TYPE 277  10   3  19
D40V12, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              50               277
  R1               2                10
  R2               1                 3
  RX               2                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
  XQ GAIN MUTATED                                  0     1
  XQ GAIN WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           7    53
  XQ GAIN WILD-TYPE                        28   314
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                      7                28
  WHITE                                         53               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"
D40V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  46
  XQ GAIN WILD-TYPE   7 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   46
  XQ GAIN WILD-TYPE    7  299
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              46               299
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    50  18
  1P LOSS WILD-TYPE 279  69
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               68               348 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               18                69 
$`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-05-5425 TCGA-38-4628 TCGA-44-3918 TCGA-44-5643 
         365          457          882         1492         1036         1013 
TCGA-44-6144 TCGA-44-A47F TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-6745 
         723          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-73-A9RS TCGA-75-7027 TCGA-78-7146 
         800           40           38          305         1956         1988 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7159 TCGA-78-7160 TCGA-80-5608 
        1944         1093          760         1221          678         1972 
TCGA-86-6851 TCGA-86-7701 TCGA-86-8054 TCGA-86-8278 TCGA-86-8669 TCGA-91-8499 
        1959           11          745          476           34           36 
TCGA-95-7043 TCGA-95-7567 TCGA-95-A4VP TCGA-97-7554 TCGA-97-8172 TCGA-97-8174 
           2          568          605          775          182         1965 
TCGA-MP-A4T7 TCGA-MP-A4TE 
        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-05-5428 TCGA-05-5429 TCGA-05-5715 
         761          730          151          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-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
        1147          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-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 
        1163          190          722          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-44-6778 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-44-7671 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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
        6443         2174         2146          785          944         1499 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 
         246          282          267         1091         2370          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-53-7813 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-55-6980 
           2          993           24         1239           25           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 
        1826         1233         1170           18          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40          705           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          462 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
         100          600           26            4           47           15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          29           11          228            9            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-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
          33           29           48         1952           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46V 
          47          162         1216         1289         2696         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-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        1126         1968           62          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-69-7763 TCGA-69-7764 TCGA-69-7765 
         141          422          202          690          414          165 
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-73-4662 TCGA-73-4668 
         129          214           61         1600          912          467 
TCGA-73-4670 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         131          164          621          519         1970         1967 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
        1965         1973         1950         1963         1202         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1957         1961         1963          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-83-5908 TCGA-86-7711 
        1981         1954         1964         1965          824          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-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 
        1963           13           24          479          489          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-86-8671 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-A4BC TCGA-91-A4BD TCGA-93-7347 
         492          505          174           44          218          297 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
         127          186           34         1973          377          477 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 
         476          830           84          121          553          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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
         435          116            6          266          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         102          827         1175           84         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1951         1954         1957         1980         1951         1944 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970          142         1955         1971         1490          121 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                 2 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             2151              6443 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            734.0             444.5 
[1] "1.0 - 2151.0 (734.0)" "2.0 - 6443.0 (444.5)"
[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       14         7        13         21
  1P LOSS WILD-TYPE       4      103      118        42        57         47
                   vv
clus                STAGE IIIB STAGE IV
  1P LOSS MUTATED            4        4
  1P LOSS WILD-TYPE          7       20
D41V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                13               103
  STAGE IB                14               118
  STAGE IIA                7                42
  STAGE IIB               13                57
  STAGE IIIA              21                47
  STAGE IIIB               4                 7
  STAGE IV                 4                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
  1P LOSS MUTATED    16  46   9   5
  1P LOSS WILD-TYPE 131 221  33  13
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              16               131
  T2              46               221
  T3               9                33
  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  18    21
  1P LOSS WILD-TYPE 264  73    53
D41V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                 37               264
  N1                 18                73
  N2+N3              21                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
  1P LOSS MUTATED    62   4   0   0  11
  1P LOSS WILD-TYPE 264  14   1   4 112
D41V6, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               62               264
  M1                4                14
  M1A               0                 1
  M1B               0                 4
  MX               11               112
[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    36  41
  1P LOSS WILD-TYPE 219 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     36   41
  1P LOSS WILD-TYPE  219  180
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              36               219
  MALE                41               180
[1] 2 2
[1] FALSE
D41V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1P LOSS MUTATED                            4
  1P LOSS WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1P LOSS MUTATED                                  20
  1P LOSS WILD-TYPE                                74
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                   43
  1P LOSS WILD-TYPE                                                260
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1P LOSS MUTATED                                            0
  1P LOSS WILD-TYPE                                          5
                   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                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  1P LOSS MUTATED                              2
  1P LOSS WILD-TYPE                            5
D41V9, multiclass
                                                    clus
vv                                                   1P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               20
  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                                        11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               260
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      5
  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  73
  1P LOSS WILD-TYPE  17 382
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4   73
  1P LOSS WILD-TYPE   17  382
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                4                17
  YES              73               382
[1] 2 2
[1] FALSE
D41V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    52   1   1   4
  1P LOSS WILD-TYPE 275  11   3  17
D41V12, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              52               275
  R1               1                11
  R2               1                 3
  RX               4                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
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           4    58
  1P LOSS WILD-TYPE                        31   309
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                      4                31
  WHITE                                         58               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"
D41V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  53
  1P LOSS WILD-TYPE   7 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   53
  1P LOSS WILD-TYPE    7  292
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              53               292
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    19   6
  1Q LOSS WILD-TYPE 310  81
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               391 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                81 
$`1Q LOSS MUTATED`
TCGA-05-4396 TCGA-05-4422 TCGA-05-4427 TCGA-44-5643 TCGA-49-4507 TCGA-49-6745 
        1947          365          791         1013          268          522 
TCGA-49-6761 TCGA-50-7109 TCGA-55-6986 TCGA-55-8090 TCGA-55-8205 TCGA-55-8507 
         354          255         2151            6           33            8 
TCGA-55-8620 TCGA-62-8402 TCGA-64-5774 TCGA-64-5778 TCGA-73-4666 TCGA-75-7027 
          66         1445         1959         1305          800         1956 
TCGA-78-7146 TCGA-86-6851 TCGA-86-8278 TCGA-91-8499 TCGA-95-7043 TCGA-97-8174 
        1988         1959          476           36            2         1965 
TCGA-MP-A4TF 
        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-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
         444          592          366          218          557         1970 
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-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         486          466          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-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
         896          157         1700          445          369          890 
TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        6443         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-53-7624 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-55-6972 TCGA-55-6980 TCGA-55-6983 
          24         1239           25         1475           67         1826 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        1233         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          705           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          462 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
         100          600           26            4           47           15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          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-55-8616 TCGA-55-8619 
         146          202          536           15           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-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
           1           28            5           47          162         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-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        1968           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-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-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
         912          467          131           40          164           38 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 
         621          519          305         1970         1967         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-78-7166 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-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 
        1964         1965         1972          824           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-91-6828 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-91-6847 
          60          310           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          505          174           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 
         218          297          127          186           34         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
         568          377          477          476          830           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         121          553          605          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-97-8175 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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
         435          116            6          266          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         102          827         1175           84         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-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1944         1970          142         1955         1971         1490 
TCGA-S2-AA1A 
         121 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                 1 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             2151              6443 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              791               466 
[1] "2.0 - 2151.0 (791.0)" "1.0 - 6443.0 (466.0)"
[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        5         3         3          8
  1Q LOSS WILD-TYPE       4      112      127        46        67         60
                   vv
clus                STAGE IIIB STAGE IV
  1Q LOSS MUTATED            1        2
  1Q LOSS WILD-TYPE         10       22
D42V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 4               112
  STAGE IB                 5               127
  STAGE IIA                3                46
  STAGE IIB                3                67
  STAGE IIIA               8                60
  STAGE IIIB               1                10
  STAGE IV                 2                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
  1Q LOSS MUTATED     8  15   2   1
  1Q LOSS WILD-TYPE 139 252  40  17
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               8               139
  T2              15               252
  T3               2                40
  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    14   6     7
  1Q LOSS WILD-TYPE 287  85    67
D42V5, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0                 14               287
  N1                  6                85
  N2+N3               7                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
  1Q LOSS MUTATED    20   1   0   1   5
  1Q LOSS WILD-TYPE 306  17   1   3 118
D42V6, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               20               306
  M1                1                17
  M1A               0                 1
  M1B               1                 3
  MX                5               118
[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  13
  1Q LOSS WILD-TYPE 241 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14   13
  1Q LOSS WILD-TYPE  241  208
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              14               241
  MALE                13               208
[1] 2 2
[1] FALSE
D42V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  1Q LOSS MUTATED                            0
  1Q LOSS WILD-TYPE                         15
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  1Q LOSS MUTATED                                   7
  1Q LOSS WILD-TYPE                                87
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                   16
  1Q LOSS WILD-TYPE                                                287
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  1Q LOSS MUTATED                                            0
  1Q LOSS WILD-TYPE                                          5
                   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                                             5
                   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)              16
  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                                        15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               287
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      5
  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  24
  1Q LOSS WILD-TYPE  18 431
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   24
  1Q LOSS WILD-TYPE   18  431
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                3                18
  YES              24               431
[1] 2 2
[1] FALSE
D42V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    17   0   0   0
  1Q LOSS WILD-TYPE 310  12   4  21
D42V12, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              17               310
  R1               0                12
  R2               0                 4
  RX               0                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   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    21
  1Q LOSS WILD-TYPE                        33   346
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                33
  WHITE                                         21               346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  20
  1Q LOSS WILD-TYPE   7 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   20
  1Q LOSS WILD-TYPE    7  325
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              20               325
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    18   2
  2P LOSS WILD-TYPE 311  85
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               20               396 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                85 
$`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-86-8074 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 
         519          760           24          181          182         1965 
TCGA-L4-A4E5 TCGA-MP-A4T8 
         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-49-AARQ TCGA-50-5045 
         369          890          522          354         6443         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-55-7727 TCGA-55-7728 TCGA-55-7815 
          40          705           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-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33          462          100            6          600 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
          26            4           47           33           46           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
         674          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-A46U TCGA-62-A46V TCGA-62-A472 
        1970         2696         1445         2067         2199          910 
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-67-3773 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-69-7973 
         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-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-73-4676 TCGA-73-4677 TCGA-73-7498 
         467          131           40          164           38          621 
TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         305         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-86-8054 
         422         1968          591         1963          508          745 
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-86-8358 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-91-6828 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-91-6847 
          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          505          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-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
           2         1973          568          377          477          476 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
         830           84          121          553          605          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-97-8175 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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
         116            6          266          312          111          102 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         827         1175           84         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE 
        1954         1954         1980         1951         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970          142         1955         1971         1490          121 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15                 1 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2151              6443 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              669               464 
[1] "15.0 - 2151.0 (669.0)" "1.0 - 6443.0 (464.0)" 
[1] "hr=" "2.6"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  2P LOSS MUTATED         2        4        9         2         3          2
  2P LOSS WILD-TYPE       3      112      123        47        67         66
                   vv
clus                STAGE IIIB STAGE IV
  2P LOSS MUTATED            0        1
  2P LOSS WILD-TYPE         11       23
D43V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                 4               112
  STAGE IB                 9               123
  STAGE IIA                2                47
  STAGE IIB                3                67
  STAGE IIIA               2                66
  STAGE IIIB               0                11
  STAGE IV                 1                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
  2P LOSS MUTATED     7  15   1   0
  2P LOSS WILD-TYPE 140 252  41  18
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               7               140
  T2              15               252
  T3               1                41
  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     2
  2P LOSS WILD-TYPE 283  88    72
D43V5, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0                 18               283
  N1                  3                88
  N2+N3               2                72
[1] 3 2
[1] 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    17   1   0   0   5
  2P LOSS WILD-TYPE 309  17   1   4 118
D43V6, multiclass
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               17               309
  M1                1                17
  M1A               0                 1
  M1B               0                 4
  MX                5               118
[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    14   9
  2P LOSS WILD-TYPE 241 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     14    9
  2P LOSS WILD-TYPE  241  212
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              14               241
  MALE                 9               212
[1] 2 2
[1] FALSE
D43V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2P LOSS MUTATED                            1
  2P LOSS WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2P LOSS MUTATED                                   4
  2P LOSS WILD-TYPE                                90
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                   13
  2P LOSS WILD-TYPE                                                290
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2P LOSS MUTATED                                            0
  2P LOSS WILD-TYPE                                          5
                   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                                             5
                   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                                4
  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                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               290
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      5
  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     0  23
  2P LOSS WILD-TYPE  21 432
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   23
  2P LOSS WILD-TYPE   21  432
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                0                21
  YES              23               432
[1] 2 2
[1] FALSE
D43V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    12   0   0   2
  2P LOSS WILD-TYPE 315  12   4  19
D43V12, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              12               315
  R1               0                12
  R2               0                 4
  RX               2                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
  2P LOSS MUTATED                                  0     1
  2P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           1    18
  2P LOSS WILD-TYPE                        34   349
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                34
  WHITE                                         18               349
[1] 4 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   7 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   17
  2P LOSS WILD-TYPE    7  328
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              17               328
[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 312  86
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               18               398 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                86 
$`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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        6443         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-50-6597 TCGA-50-7109 
         653          567          883          764         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-55-6712 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-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        1233         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          705           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          462 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
         100            6          600           26            4           47 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          33           46           66          674          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-62-8398 TCGA-62-8399 TCGA-62-8402 
          47          162         1216         1970         2696         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-64-1679 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-69-7761 TCGA-69-7763 
         385          174          141          422          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-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 
         382          100           77          129          214         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-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 
         164           38          621          305         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-78-7220 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-86-6851 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-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
        1963          508           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          505 
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-95-7562 TCGA-95-7567 TCGA-95-7944 
         186           34            2         1973          568          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
         477          476          830           84          121          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         605          964         1965         1932         1332           22 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
         107         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-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 
         238          435          116            6          266          312 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         111          102          827         1175           84         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 TCGA-S2-AA1A 
        1490          121 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15                 1 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2151              6443 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              632               464 
[1] "15.0 - 2151.0 (632.0)" "1.0 - 6443.0 (464.0)" 
[1] "hr=" "3.8"
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       4      112      123        48        66         65
                   vv
clus                STAGE IIIB STAGE IV
  2Q LOSS MUTATED            0        1
  2Q LOSS WILD-TYPE         11       23
D44V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                 4               112
  STAGE IB                 9               123
  STAGE IIA                1                48
  STAGE IIB                4                66
  STAGE IIIA               3                65
  STAGE IIIB               0                11
  STAGE IV                 1                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
  2Q LOSS MUTATED     6  15   2   0
  2Q LOSS WILD-TYPE 141 252  40  18
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               6               141
  T2              15               252
  T3               2                40
  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 284  88    71
D44V5, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0                 17               284
  N1                  3                88
  N2+N3               3                71
[1] 3 2
[1] 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 308  17   1   4 119
D44V6, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               18               308
  M1                1                17
  M1A               0                 1
  M1B               0                 4
  MX                4               119
[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 241 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     14    9
  2Q LOSS WILD-TYPE  241  212
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              14               241
  MALE                 9               212
[1] 2 2
[1] FALSE
D44V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  2Q LOSS MUTATED                            3
  2Q LOSS WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  2Q LOSS MUTATED                                   4
  2Q LOSS WILD-TYPE                                90
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                   11
  2Q LOSS WILD-TYPE                                                292
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  2Q LOSS MUTATED                                            0
  2Q LOSS WILD-TYPE                                          5
                   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                                             5
                   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                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      5
  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  21 432
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   23
  2Q LOSS WILD-TYPE   21  432
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                0                21
  YES              23               432
[1] 2 2
[1] FALSE
D44V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    13   0   0   1
  2Q LOSS WILD-TYPE 314  12   4  20
D44V12, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              13               314
  R1               0                12
  R2               0                 4
  RX               1                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                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                        34   350
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                34
  WHITE                                         17               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  15
  2Q LOSS WILD-TYPE   7 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   15
  2Q LOSS WILD-TYPE    7  330
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              15               330
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   138  33
  3P LOSS WILD-TYPE 191  54
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              171               245 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               33                54 
$`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          705           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-73-A9RS TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 
         305         1970         1956         1965         1988         1944 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        1221          678         1937         1965         1972         1949 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-83-5908 
         327         1952         1949         1954         1972          824 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7954 TCGA-86-8054 TCGA-86-8073 
        1959           11          422         1963          745           13 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 
         476           16           19           35           34           30 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 
        1940           60          310           79          842          224 
TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 
         492           36           44          127           34            2 
TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 
         568          477          476          830          605          964 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M7 TCGA-J2-8192 
         775          181         1965          147          271          154 
TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MP-A4T8 
         114          238          578          266          111         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-49-AARQ TCGA-50-5045 
         157          369          522          354         6443         2174 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5933 TCGA-50-5942 
         455          785          944          282         2370          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ 
         764          686          255          105          424          280 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
         701           87            2          993           24         1239 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
          25         1475           67         2151         1170           18 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
         121           95           39           24           54           19 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
          21           31            5           33          462          100 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 
         600           26           47           15           33           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 
         674          216           44           23           29          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
           9            3          146           49          106           33 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8402 
          42           48           28            5         1216         1445 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 
        2067         2199          910          628         1686         1126 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
        1968           62         1305          427          385          174 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
         141          202          186          184           70          382 
TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 TCGA-73-4668 TCGA-73-4676 
          77          129          214         1600          467          164 
TCGA-73-4677 TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
          38         1967         1973         1950         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-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 TCGA-78-7540 
         215         1940         1950         1934         1944          881 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-86-7711 
         994         1971         1981         1964         1965          630 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
        1968          591          508           10         1963           24 
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-86-8671 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-91-6836 TCGA-91-6840 TCGA-91-6849 TCGA-91-8496 
          39          323          417          372           35          505 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7562 TCGA-95-7944 
         174          218          297          186         1973          377 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
          84          121          553         1965         1932         1332 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 
          22          107          182           87           15          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-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
         170          287          282          435          116            6 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         312          102          827         1175           84         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 TCGA-S2-AA1A 
        1970          142         1971         1490          121 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                 2 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             2696              6443 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              573               427 
[1] "1.0 - 2696.0 (573.0)" "2.0 - 6443.0 (427.0)"
[1] "hr=" "1.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  3P LOSS MUTATED         1       44       50        25        32         32
  3P LOSS WILD-TYPE       4       72       82        24        38         36
                   vv
clus                STAGE IIIB STAGE IV
  3P LOSS MUTATED            3       12
  3P LOSS WILD-TYPE          8       12
D45V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                44                72
  STAGE IB                50                82
  STAGE IIA               25                24
  STAGE IIB               32                38
  STAGE IIIA              32                36
  STAGE IIIB               3                 8
  STAGE IV                12                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
  3P LOSS MUTATED    61 121  12   4
  3P LOSS WILD-TYPE  86 146  30  14
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              61                86
  T2             121               146
  T3              12                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
  3P LOSS MUTATED   118  42    35
  3P LOSS WILD-TYPE 183  49    39
D45V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                118               183
  N1                 42                49
  N2+N3              35                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   137   9   0   2  50
  3P LOSS WILD-TYPE 189   9   1   2  73
D45V6, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              137               189
  M1                9                 9
  M1A               0                 1
  M1B               2                 2
  MX               50                73
[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   104  95
  3P LOSS WILD-TYPE 151 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    104   95
  3P LOSS WILD-TYPE  151  126
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             104               151
  MALE                95               126
[1] 2 2
[1] FALSE
D45V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3P LOSS MUTATED                            7
  3P LOSS WILD-TYPE                          8
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3P LOSS MUTATED                                  45
  3P LOSS WILD-TYPE                                49
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                  127
  3P LOSS WILD-TYPE                                                176
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3P LOSS MUTATED                                            0
  3P LOSS WILD-TYPE                                          5
                   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                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  3P LOSS MUTATED                              4
  3P LOSS WILD-TYPE                            3
D45V9, multiclass
                                                    clus
vv                                                   3P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             127
  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)               176
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      4
  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     9 190
  3P LOSS WILD-TYPE  12 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      9  190
  3P LOSS WILD-TYPE   12  265
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                9                12
  YES             190               265
[1] 2 2
[1] FALSE
D45V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED   135   2   1   5
  3P LOSS WILD-TYPE 192  10   3  16
D45V12, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0             135               192
  R1               2                10
  R2               1                 3
  RX               5                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
  3P LOSS MUTATED                                  0     3
  3P LOSS WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          18   155
  3P LOSS WILD-TYPE                        17   212
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                     18                17
  WHITE                                        155               212
[1] 4 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     2 153
  3P LOSS WILD-TYPE   5 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2  153
  3P LOSS WILD-TYPE    5  192
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO             153               192
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    97  20
  3Q LOSS WILD-TYPE 232  67
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              117               299 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               20                67 
$`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-73-A9RS TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7148 
         621          305         1970         1956         1965         1944 
TCGA-78-7160 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7539 TCGA-78-8660 
         678         1937         1965         1972          327         1954 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7713 TCGA-86-7954 TCGA-86-8054 
        1972          824         1959          422         1963          745 
TCGA-86-8073 TCGA-86-8280 TCGA-86-8585 TCGA-86-A4D0 TCGA-91-6847 TCGA-91-6848 
          13           16           35           30          842          224 
TCGA-91-7771 TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VK 
         492          127           34          568          476          121 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 
         605          964          775          181          182         1965 
TCGA-97-8177 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A50W 
         147          154          114          238          578          266 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TI 
        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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         522          354         6443         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
         785          944          246          282          267         2370 
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-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
        1986         1971          424          280          701         1178 
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-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 
        1233         2151         1170           18          121            6 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
          95          705           39           39           24           54 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
          19           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
         462          100          600           26           47           15 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          33           66          674          216           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
          29           11            8          228            9            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-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8402 
          48         1952           28            5         1216         1445 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 
        2067         2199         1246          910          628         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3773 
        1126         1968           62         1305          866          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 
         385          174          141          202          186          230 
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-73-4658 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
        1600          467          131          164           38          519 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
        1967         1973         1988         1950         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-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7536 
        1221          215         1940         1950         1934         1949 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
        1944          881         1952          994         1949         1971 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
        1981         1964         1965           11          630         1968 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
         591          508           10         1963           24          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         489          476          482         1955           19           26 
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-91-6836 TCGA-91-6840 TCGA-91-6849 TCGA-91-8496 
         310           79          417          372           35          505 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 
         174           36           44          218          297          186 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 
           2         1973          377          477          830           84 
TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 
         553         1965         1932         1332           22          107 
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-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
         392          427          459           44          170          287 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV 
         282          435          116            6          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         102          827         1175           84         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 TCGA-S2-AA1A 
        1970          142         1971         1490          121 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                 2 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             2696              6443 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              568               459 
[1] "1.0 - 2696.0 (568.0)" "2.0 - 6443.0 (459.0)"
[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        16        25         26
  3Q LOSS WILD-TYPE       4       88      101        33        45         42
                   vv
clus                STAGE IIIB STAGE IV
  3Q LOSS MUTATED            3        7
  3Q LOSS WILD-TYPE          8       17
D46V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                28                88
  STAGE IB                31               101
  STAGE IIA               16                33
  STAGE IIB               25                45
  STAGE IIIA              26                42
  STAGE IIIB               3                 8
  STAGE IV                 7                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
  3Q LOSS MUTATED    40  83  10   4
  3Q LOSS WILD-TYPE 107 184  32  14
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              40               107
  T2              83               184
  T3              10                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
  3Q LOSS MUTATED    77  31    29
  3Q LOSS WILD-TYPE 224  60    45
D46V5, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0                 77               224
  N1                 31                60
  N2+N3              29                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    99   4   0   2  32
  3Q LOSS WILD-TYPE 227  14   1   2  91
D46V6, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               99               227
  M1                4                14
  M1A               0                 1
  M1B               2                 2
  MX               32                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"
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    71  66
  3Q LOSS WILD-TYPE 184 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     71   66
  3Q LOSS WILD-TYPE  184  155
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              71               184
  MALE                66               155
[1] 2 2
[1] FALSE
D46V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  3Q LOSS MUTATED                            6
  3Q LOSS WILD-TYPE                          9
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  3Q LOSS MUTATED                                  33
  3Q LOSS WILD-TYPE                                61
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                   80
  3Q LOSS WILD-TYPE                                                223
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  3Q LOSS MUTATED                                            0
  3Q LOSS WILD-TYPE                                          5
                   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                                             4
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  3Q LOSS MUTATED                              4
  3Q LOSS WILD-TYPE                            3
D46V9, multiclass
                                                    clus
vv                                                   3Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              80
  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                                         9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               223
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      4
  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     6 131
  3Q LOSS WILD-TYPE  15 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6  131
  3Q LOSS WILD-TYPE   15  324
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                6                15
  YES             131               324
[1] 2 2
[1] FALSE
D46V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    89   1   0   5
  3Q LOSS WILD-TYPE 238  11   4  16
D46V12, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              89               238
  R1               1                11
  R2               0                 4
  RX               5                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
  3Q LOSS MUTATED                                  0     3
  3Q LOSS WILD-TYPE                                1     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                          15   103
  3Q LOSS WILD-TYPE                        20   264
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                     15                20
  WHITE                                        103               264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0 107
  3Q LOSS WILD-TYPE   7 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0  107
  3Q LOSS WILD-TYPE    7  238
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO             107               238
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    82  12
  4P LOSS WILD-TYPE 247  75
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               94               322 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               12                75 
$`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          705           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-95-A4VN TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD 
         568          377          553          427          170          287 
TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
         578          111          102         1175 

$`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-49-AARQ TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 
         522          354         6443         2174          785         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-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 
        1986          424          701         1178         1479           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 
           2          993           24         1239         1475           67 
TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1826         2151         1170           18           35          121 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 
           6            4           39           34           24           19 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
          16           21            3           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
         462          100            6          600           26            4 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
          47           15           33           46           66          674 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
         216           44           23           11           15          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
           9            3          146           49           66          106 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          33           42           48            1           28            5 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 
        1216         1289         2696         1445         2199         1246 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
        1728         1189         1686         1126         1968         1959 
TCGA-64-5775 TCGA-64-5781 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
          62         1559           31          573          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
         174          141          422          202          186          414 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
         165          184           70          382          100           77 
TCGA-69-8255 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 
         129         1600          912          800          467          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 
          38          621          519          305         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-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1961         1963          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1965         1972         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-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
         630         1968          591          508          745         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
          13           24          489          476          482           16 
TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
        1955           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-91-6835 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          505          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 
         297          127          186           34         1973          477 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 
         476          830           84          121          605          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-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
         148          115          197          271          392          459 
TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
          44          154          114          282          238          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N5 
         116            6          266          312          827           84 
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-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 TCGA-S2-AA1A 
        1955         1971         1490          121 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                 1 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2146              6443 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            544.5             464.0 
[1] "2.0 - 2146.0 (544.5)" "1.0 - 6443.0 (464.0)"
[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       35         9        14         17
  4P LOSS WILD-TYPE       4       92       97        40        56         51
                   vv
clus                STAGE IIIB STAGE IV
  4P LOSS MUTATED            5        5
  4P LOSS WILD-TYPE          6       19
D47V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                24                92
  STAGE IB                35                97
  STAGE IIA                9                40
  STAGE IIB               14                56
  STAGE IIIA              17                51
  STAGE IIIB               5                 6
  STAGE IV                 5                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
  4P LOSS MUTATED    31  63  10   4
  4P LOSS WILD-TYPE 116 204  32  14
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              31               116
  T2              63               204
  T3              10                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
  4P LOSS MUTATED    68  17    21
  4P LOSS WILD-TYPE 233  74    53
D47V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                 68               233
  N1                 17                74
  N2+N3              21                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
  4P LOSS MUTATED    74   5   0   0  30
  4P LOSS WILD-TYPE 252  13   1   4  93
D47V6, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               74               252
  M1                5                13
  M1A               0                 1
  M1B               0                 4
  MX               30                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"
D47V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    56  54
  4P LOSS WILD-TYPE 199 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     56   54
  4P LOSS WILD-TYPE  199  167
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              56               199
  MALE                54               167
[1] 2 2
[1] FALSE
D47V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4P LOSS MUTATED                            3
  4P LOSS WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4P LOSS MUTATED                                  22
  4P LOSS WILD-TYPE                                72
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                   74
  4P LOSS WILD-TYPE                                                229
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4P LOSS MUTATED                                            0
  4P LOSS WILD-TYPE                                          5
                   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                                               2
  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)              74
  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                    2
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   4P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 72
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               229
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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     6 104
  4P LOSS WILD-TYPE  15 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6  104
  4P LOSS WILD-TYPE   15  351
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                6                15
  YES             104               351
[1] 2 2
[1] FALSE
D47V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED    74   3   1   8
  4P LOSS WILD-TYPE 253   9   3  13
D47V12, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              74               253
  R1               3                 9
  R2               1                 3
  RX               8                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
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          12    79
  4P LOSS WILD-TYPE                        23   288
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                     12                23
  WHITE                                         79               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"
D47V14, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  83
  4P LOSS WILD-TYPE   6 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   83
  4P LOSS WILD-TYPE    6  262
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              83               262
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    91  17
  4Q LOSS WILD-TYPE 238  70
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              108               308 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               17                70 
$`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          705           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-95-A4VN 
         372          842            2          568          377          553 
TCGA-95-A4VP TCGA-97-7937 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
         605          181          427           44          170          287 
TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4TA TCGA-MP-A4TF 
         578          111          102         1175         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-49-AARQ TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 
         354         6443         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-50-8460 TCGA-53-7624 TCGA-53-7626 
         883          764         1015          105         1986         1971 
TCGA-53-7813 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
         424         1479           87            2          993           24 
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-55-7725 
        1170           18           35          121            6           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 
          34           24           19           16           21            3 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          31            5           33          462          100            6 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
         600           47           15           33           46           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 
         674          216           44           23           11          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 
           9            3          146          536           15           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
          66          106           33           48           28            5 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V 
         162         1216         1289         2696         1445         2199 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 
        1246         1728         1189         1126         1959           62 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        1559          866           31          573          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-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K 
         184           70          382          100           77          214 
TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
        1600          800          467          164           38          621 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 
         519          305         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-78-7160 TCGA-78-7161 
        1948         1957         1961         1963          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 
        1940         1950         1934         1965         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-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
         630         1968          591          745         1963           13 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 
          24          489          476           16         1955           19 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
          26           35           45           18          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          505          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-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
          34         1973          477          476          830           84 
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-L9-A50W TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N5 
         116            6          266          312          827           84 
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-A4TC TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1980         1944         1970          142         1955         1971 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                 2 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             2146              6443 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              497               464 
[1] "1.0 - 2146.0 (497.0)" "2.0 - 6443.0 (464.0)"
[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       34        12        10         22
  4Q LOSS WILD-TYPE       3       84       98        37        60         46
                   vv
clus                STAGE IIIB STAGE IV
  4Q LOSS MUTATED            5        8
  4Q LOSS WILD-TYPE          6       16
D48V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  2                 3
  STAGE IA                32                84
  STAGE IB                34                98
  STAGE IIA               12                37
  STAGE IIB               10                60
  STAGE IIIA              22                46
  STAGE IIIB               5                 6
  STAGE IV                 8                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
  4Q LOSS MUTATED    38  71   9   5
  4Q LOSS WILD-TYPE 109 196  33  13
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              38               109
  T2              71               196
  T3               9                33
  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    80  15    26
  4Q LOSS WILD-TYPE 221  76    48
D48V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0                 80               221
  N1                 15                76
  N2+N3              26                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
  4Q LOSS MUTATED    83   7   0   1  32
  4Q LOSS WILD-TYPE 243  11   1   3  91
D48V6, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               83               243
  M1                7                11
  M1A               0                 1
  M1B               1                 3
  MX               32                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"
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    64  61
  4Q LOSS WILD-TYPE 191 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     64   61
  4Q LOSS WILD-TYPE  191  160
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              64               191
  MALE                61               160
[1] 2 2
[1] FALSE
D48V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  4Q LOSS MUTATED                            4
  4Q LOSS WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  4Q LOSS MUTATED                                  21
  4Q LOSS WILD-TYPE                                73
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                   88
  4Q LOSS WILD-TYPE                                                215
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  4Q LOSS MUTATED                                            0
  4Q LOSS WILD-TYPE                                          5
                   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                                               2
  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                                       4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              88
  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                    2
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   4Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                        11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               215
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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     6 119
  4Q LOSS WILD-TYPE  15 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      6  119
  4Q LOSS WILD-TYPE   15  336
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                6                15
  YES             119               336
[1] 2 2
[1] FALSE
D48V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED    83   4   2   8
  4Q LOSS WILD-TYPE 244   8   2  13
D48V12, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              83               244
  R1               4                 8
  R2               2                 2
  RX               8                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
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                          12    93
  4Q LOSS WILD-TYPE                        23   274
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                     12                23
  WHITE                                         93               274
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     2  94
  4Q LOSS WILD-TYPE   5 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   94
  4Q LOSS WILD-TYPE    5  251
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 5
  NOT HISPANIC OR LATINO              94               251
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    32   2
  5P LOSS WILD-TYPE 297  85
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               34               382 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                85 
$`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-44-7662 TCGA-49-6742 TCGA-55-1596 TCGA-55-7281 
         723          328          218          445         1375           18 
TCGA-55-7914 TCGA-55-8505 TCGA-55-A492 TCGA-62-8398 TCGA-64-5779 TCGA-67-3771 
           3           29            1         1970          864          610 
TCGA-67-3772 TCGA-69-7979 TCGA-69-8255 TCGA-73-A9RS TCGA-75-7027 TCGA-78-7160 
         573           89          129          305         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-95-7567 TCGA-97-8175 TCGA-MN-A4N1 TCGA-MN-A4N4 
         568           87          827         1175 

$`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-44-7667 
        1864         1978          444          592          366          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-49-6743 
         999          268          896          157         1700          369 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 
         890          522          354         6443         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-53-7624 
         764          686         1015          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-55-5899 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-55-7283 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 
         705           39           39           34           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
          19           16          197           21           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33          462          100            6          600           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-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
         674          216           44           23           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-A493 
          33           42           29           48         1952           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-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-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 
          62         1305         1559          866           31          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-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
         382          100           77          214           61         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-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 
         164           38          621          519         1970         1967 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        1965         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-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
        1963         1221         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-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-86-8075 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-91-6830 TCGA-91-6831 
          30           14           39          323           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          505          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 
         297          127          186           34         1973          377 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
         477          476          830           84          121          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         605          964         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-97-8547 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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 
           6          266          312          111          102           84 
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-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 TCGA-S2-AA1A 
        1955         1971         1490          121 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                 2 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1970              6443 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            476.5             476.0 
[1] "1.0 - 1970.0 (476.5)" "2.0 - 6443.0 (476.0)"
[1] "hr=" "1.8"
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       5      106      121        45        62         65
                   vv
clus                STAGE IIIB STAGE IV
  5P LOSS MUTATED            0        2
  5P LOSS WILD-TYPE         11       22
D49V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                10               106
  STAGE IB                11               121
  STAGE IIA                4                45
  STAGE IIB                8                62
  STAGE IIIA               3                65
  STAGE IIIB               0                11
  STAGE IV                 2                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
  5P LOSS MUTATED    13  21   2   1
  5P LOSS WILD-TYPE 134 246  40  17
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              13               134
  T2              21               246
  T3               2                40
  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    25   9     4
  5P LOSS WILD-TYPE 276  82    70
D49V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                 25               276
  N1                  9                82
  N2+N3               4                70
[1] 3 2
[1] 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    29   2   0   0   7
  5P LOSS WILD-TYPE 297  16   1   4 116
D49V6, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               29               297
  M1                2                16
  M1A               0                 1
  M1B               0                 4
  MX                7               116
[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    12  26
  5P LOSS WILD-TYPE 243 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     12   26
  5P LOSS WILD-TYPE  243  195
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              12               243
  MALE                26               195
[1] 2 2
[1] FALSE
D49V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5P LOSS MUTATED                            2
  5P LOSS WILD-TYPE                         13
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5P LOSS MUTATED                                   9
  5P LOSS WILD-TYPE                                85
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                   23
  5P LOSS WILD-TYPE                                                280
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5P LOSS MUTATED                                            0
  5P LOSS WILD-TYPE                                          5
                   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                                             3
                   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                                9
  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                                    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                                        13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               280
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      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"
D49V10, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     1  37
  5P LOSS WILD-TYPE  20 418
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   37
  5P LOSS WILD-TYPE   20  418
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                1                20
  YES              37               418
[1] 2 2
[1] FALSE
D49V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    24   1   0   2
  5P LOSS WILD-TYPE 303  11   4  19
D49V12, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              24               303
  R1               1                11
  R2               0                 4
  RX               2                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
  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                        32   339
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                32
  WHITE                                         28               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"
D49V14, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     1  28
  5P LOSS WILD-TYPE   6 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   28
  5P LOSS WILD-TYPE    6  317
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              28               317
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   104  17
  5Q LOSS WILD-TYPE 225  70
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              121               295 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               17                70 
$`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-55-8094 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
           3            4           23           29           11            8 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
         228            9           15           48           66           42 
TCGA-55-A491 TCGA-55-A492 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        1952            1         1216         1970         2696         1445 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 
        1246         1728         1686         1968         1305          864 
TCGA-67-3771 TCGA-67-3772 TCGA-69-7765 TCGA-69-7979 TCGA-69-8255 TCGA-71-6725 
         610          573          165           89          129           61 
TCGA-73-4668 TCGA-73-A9RS TCGA-75-7027 TCGA-78-7149 TCGA-78-7150 TCGA-78-7159 
         467          305         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-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4TC TCGA-MP-A4TE 
           6          111          827         1175         1944         1970 
TCGA-MP-A5C7 
        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-49-AARQ TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 
         522          354         6443          455          785          246 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 
         282          267         1091         2370          653          883 
TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
         764         1015          255          105         1971          424 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 
        1479            2          993           24           25         1475 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 
          67         1826         2151         1170           35          121 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 
           4           95           40          705           39           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
          54           19          197           21           31            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
          33          462          100            6          600           26 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
          47           15           33           46           66          674 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
         216           44           15            3          146          202 
TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 
         536           49          106           33           29           48 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-A46U 
          28            5           47          162         1289         2067 
TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 
        2199          910          628         1189         1126         1959 
TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 
          62         1559          866           31          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-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
         414          230          184           70          382          100 
TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
          77          214         1600          711          912          800 
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-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1970         1967         1965         1973         1988         1950 
TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1944         1202          760         1948         1957         1961 
TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 
        1963         1940         1950         1934         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-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
        1972          824           11          630         1968         1963 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
         745           10         1963          479          489          476 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 
          16         1955           19           26           45           34 
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-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
          39          323           60          310           79          417 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         842          224           35          492          505          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7562 TCGA-95-7944 
          44          218          297          127         1973          377 
TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
         477          830           84          121          553          605 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 
         964         1965         1932         1332          775           22 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
         107          182         1965          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-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-L9-A443 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N5 
         435          116          266          312          102           84 
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-A4TA TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK 
        1980         1951         1970          142         1955         1971 
TCGA-S2-AA1A 
         121 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                 2 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2696              6443 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              568               455 
[1] "1.0 - 2696.0 (568.0)" "2.0 - 6443.0 (455.0)"
[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        14        23         15
  5Q LOSS WILD-TYPE       5       86       92        35        47         53
                   vv
clus                STAGE IIIB STAGE IV
  5Q LOSS MUTATED            3        7
  5Q LOSS WILD-TYPE          8       17
D50V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                30                86
  STAGE IB                40                92
  STAGE IIA               14                35
  STAGE IIB               23                47
  STAGE IIIA              15                53
  STAGE IIIB               3                 8
  STAGE IV                 7                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 LOSS MUTATED    39  76  11   5
  5Q LOSS WILD-TYPE 108 191  31  13
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              39               108
  T2              76               191
  T3              11                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
  5Q LOSS MUTATED    85  29    17
  5Q LOSS WILD-TYPE 216  62    57
D50V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                 85               216
  N1                 29                62
  N2+N3              17                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  5Q LOSS MUTATED    90   4   0   2  35
  5Q LOSS WILD-TYPE 236  14   1   2  88
D50V6, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               90               236
  M1                4                14
  M1A               0                 1
  M1B               2                 2
  MX               35                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"
D50V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    57  75
  5Q LOSS WILD-TYPE 198 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     57   75
  5Q LOSS WILD-TYPE  198  146
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              57               198
  MALE                75               146
[1] 2 2
[1] FALSE
D50V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  5Q LOSS MUTATED                            4
  5Q LOSS WILD-TYPE                         11
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  5Q LOSS MUTATED                                  31
  5Q LOSS WILD-TYPE                                63
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                   83
  5Q LOSS WILD-TYPE                                                220
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  5Q LOSS MUTATED                                            0
  5Q LOSS WILD-TYPE                                          5
                   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                                             2
                   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)              83
  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                                        11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 63
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               220
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      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"
D50V10, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     4 128
  5Q LOSS WILD-TYPE  17 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4  128
  5Q LOSS WILD-TYPE   17  327
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                4                17
  YES             128               327
[1] 2 2
[1] FALSE
D50V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    88   3   0  10
  5Q LOSS WILD-TYPE 239   9   4  11
D50V12, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              88               239
  R1               3                 9
  R2               0                 4
  RX              10                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
  5Q LOSS MUTATED                                  1     3
  5Q LOSS WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          12    98
  5Q LOSS WILD-TYPE                        23   269
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                     12                23
  WHITE                                         98               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"
D50V14, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5  96
  5Q LOSS WILD-TYPE   2 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5   96
  5Q LOSS WILD-TYPE    2  249
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO              96               249
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    62  25
  6P LOSS WILD-TYPE 267  62
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               87               329 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               25                62 
$`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          705           54 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 
         100            6          600           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-73-A9RS TCGA-75-7025 
         214          711          800           40          305         1967 
TCGA-78-7146 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7158 TCGA-78-7535 
        1988         1202          760         1948         1963         1972 
TCGA-78-7536 TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 
        1949          824           11          422          591          508 
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-95-7567 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-8174 
         568          476           84          605         1965         1965 
TCGA-97-8547 TCGA-99-7458 TCGA-J2-8192 TCGA-MN-A4N1 TCGA-MP-A4T2 TCGA-MP-A4TC 
         148          392          154          827         1951         1944 
TCGA-MP-A4TF TCGA-MP-A4TK TCGA-MP-A5C7 
        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-49-AARQ TCGA-50-5045 TCGA-50-5049 
         369          890          354         6443         2174         2146 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
         785          944          246          282          267         2370 
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-55-6980 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 
          67         2151         1170           18          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
           4           95           39           39           34           24 
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-55-8092 TCGA-55-8094 TCGA-55-8096 
           5           33          462           26            4           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          15           33           46          674          216           44 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
          29            8          228            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-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          42           29           48         1952            1           28 
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-64-1677 TCGA-64-1678 TCGA-64-1679 
        2067         2199         1246          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-64-5815 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-69-7761 TCGA-69-7763 TCGA-69-7764 
         174          141          422          186          690          414 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 
         165          230           70           89          382          129 
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-73-4677 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-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7155 
        1973         1950         1944         1093         1963         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-78-7537 TCGA-78-7539 TCGA-78-7540 
        1934         1937         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-86-6851 TCGA-86-7711 TCGA-86-7714 
        1964         1965         1972         1959          630         1968 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
        1963          745           10         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-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
          19           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-91-6835 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-91-8499 
         224           35          492          505          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 
          44          218          186           34         1973          377 
TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7552 
         477          830          121          553          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-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
          87          147           15          115          197          271 
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-A443 TCGA-L9-A444 
         282          238          578          435          116            6 
TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
         266          312          111          102         1175           84 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
        1946         1967         1954         1954         1957         1980 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-S2-AA1A 
        1951         1970          142         1955          121 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                 1 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             1997              6443 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              568               462 
[1] "2.0 - 1997.0 (568.0)" "1.0 - 6443.0 (462.0)"
[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         9        15         20
  6P LOSS WILD-TYPE       5      102      100        40        55         48
                   vv
clus                STAGE IIIB STAGE IV
  6P LOSS MUTATED            3        4
  6P LOSS WILD-TYPE          8       20
D51V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                14               102
  STAGE IB                32               100
  STAGE IIA                9                40
  STAGE IIB               15                55
  STAGE IIIA              20                48
  STAGE IIIB               3                 8
  STAGE IV                 4                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
  6P LOSS MUTATED    20  62  11   4
  6P LOSS WILD-TYPE 127 205  31  14
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              20               127
  T2              62               205
  T3              11                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
  6P LOSS MUTATED    58  18    20
  6P LOSS WILD-TYPE 243  73    54
D51V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0                 58               243
  N1                 18                73
  N2+N3              20                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
  6P LOSS MUTATED    66   4   0   0  26
  6P LOSS WILD-TYPE 260  14   1   4  97
D51V6, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               66               260
  M1                4                14
  M1A               0                 1
  M1B               0                 4
  MX               26                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"
D51V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    49  49
  6P LOSS WILD-TYPE 206 172
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     49   49
  6P LOSS WILD-TYPE  206  172
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              49               206
  MALE                49               172
[1] 2 2
[1] FALSE
D51V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6P LOSS MUTATED                            3
  6P LOSS WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6P LOSS MUTATED                                  19
  6P LOSS WILD-TYPE                                75
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                   66
  6P LOSS WILD-TYPE                                                237
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6P LOSS MUTATED                                            0
  6P LOSS WILD-TYPE                                          5
                   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                                             4
                   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                               19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              66
  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                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 75
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               237
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      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"
D51V10, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  93
  6P LOSS WILD-TYPE  16 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   93
  6P LOSS WILD-TYPE   16  362
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                5                16
  YES              93               362
[1] 2 2
[1] FALSE
D51V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    68   3   1   4
  6P LOSS WILD-TYPE 259   9   3  17
D51V12, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              68               259
  R1               3                 9
  R2               1                 3
  RX               4                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
  6P LOSS MUTATED                                  0     0
  6P LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           7    79
  6P LOSS WILD-TYPE                        28   288
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                      7                28
  WHITE                                         79               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"
D51V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  72
  6P LOSS WILD-TYPE   6 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   72
  6P LOSS WILD-TYPE    6  273
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              72               273
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   135  46
  6Q LOSS WILD-TYPE 194  41
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              181               235 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               46                41 
$`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-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 
         761          882          670           30           14          182 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 
         354         1357          448         1429         1367         1280 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3918 TCGA-44-5644 TCGA-44-6147 TCGA-44-6774 
          97          246         1036          863          845          658 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-8117 TCGA-44-8120 
         705         1942         1978          444          385          260 
TCGA-44-A47F TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 
         337           76         1932         1081          428          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-50-5051 TCGA-50-5068 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         455         1499         1091         2370          653          567 
TCGA-50-5942 TCGA-50-5946 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1595 
         883          686         1986         1971          424         1479 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 
           2          993           25         1475         1826         1233 
TCGA-55-7283 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7815 TCGA-55-7903 
          35           40          705           39           54           19 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 
          21            3           31           33          100            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 
         600            4           66           23           11           15 
TCGA-55-8512 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A494 
           3           15           48           33           42            5 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 
        1216         1970         1445         2199          910         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
         628         1189         1959          864         1559          866 
TCGA-67-3771 TCGA-67-6216 TCGA-69-7760 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         610          141          202          230          184           70 
TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
         100           77          214         1600          711          800 
TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 
          40          621          519          305         1970         1967 
TCGA-75-7027 TCGA-78-7146 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1956         1988         1093         1202          760         1948 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7535 TCGA-78-7536 
        1961         1963         1221         1940         1972         1949 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8655 TCGA-80-5607 
        1944          881         1952          994         1981         1965 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
         824           11          422         1968          591          508 
TCGA-86-8054 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         745          482           16         1955           19           26 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-91-6831 TCGA-91-7771 TCGA-91-A4BD 
          15          405           10          310          492          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 TCGA-95-8494 
         297          127            2          568          476           84 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 
         553          605         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-L9-A50W TCGA-MN-A4N1 TCGA-MN-A4N5 
         578          116            6          266          827           84 
TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK 
        1946         1951         1944         1970         1970         1971 
TCGA-MP-A5C7 
        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-05-5715 TCGA-35-4122 
         761          730          457          151           62          225 
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-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 
        1073         1971          133         1324          400          741 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1301         1130         1163          190          722         1013 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 
         383          723          328          302          704         1938 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
        1864          592          366          218          557         1970 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
         882          535          719           99          486          466 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4501 TCGA-49-4506 TCGA-49-6742 
         287          351          415         1421          999          445 
TCGA-49-6743 TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         369         6443         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          462           26 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
          47           15           33           46          674          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 
          44           29            8          228            9          146 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Z 
         202          536           49           66          106           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-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A471 TCGA-64-1679 TCGA-64-1680 
        1289         2696         2067         1246         1686         1126 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
        1968           62         1305           31          573          427 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
         385          174          422          186          690          414 
TCGA-69-7765 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4662 
         165           89          382          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          505          174           36           44          186 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK 
          34         1973          377          477          830          121 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
         964         1932         1332           22          107          182 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-99-8025 TCGA-99-8028 
          87          147           15          115          427          459 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
          44          170          287          282          238          435 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T4 
         312          111          102         1175         1967         1954 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A4TI 
        1954         1957         1980         1951          142         1955 
TCGA-S2-AA1A 
         121 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                 1 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             2370              6443 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              607               422 
[1] "2.0 - 2370.0 (607.0)" "1.0 - 6443.0 (422.0)"
[1] "hr=" "1.3"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  6Q LOSS MUTATED         1       42       57        22        27         35
  6Q LOSS WILD-TYPE       4       74       75        27        43         33
                   vv
clus                STAGE IIIB STAGE IV
  6Q LOSS MUTATED            6       10
  6Q LOSS WILD-TYPE          5       14
D52V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                42                74
  STAGE IB                57                75
  STAGE IIA               22                27
  STAGE IIB               27                43
  STAGE IIIA              35                33
  STAGE IIIB               6                 5
  STAGE IV                10                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
  6Q LOSS MUTATED    58 113  21   8
  6Q LOSS WILD-TYPE  89 154  21  10
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              58                89
  T2             113               154
  T3              21                21
  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   122  38    36
  6Q LOSS WILD-TYPE 179  53    38
D52V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                122               179
  N1                 38                53
  N2+N3              36                38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  6Q LOSS MUTATED   137   8   0   2  51
  6Q LOSS WILD-TYPE 189  10   1   2  72
D52V6, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              137               189
  M1                8                10
  M1A               0                 1
  M1B               2                 2
  MX               51                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"
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   101 100
  6Q LOSS WILD-TYPE 154 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    101  100
  6Q LOSS WILD-TYPE  154  121
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE             101               154
  MALE               100               121
[1] 2 2
[1] FALSE
D52V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  6Q LOSS MUTATED                            6
  6Q LOSS WILD-TYPE                          9
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  6Q LOSS MUTATED                                  46
  6Q LOSS WILD-TYPE                                48
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                  124
  6Q LOSS WILD-TYPE                                                179
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  6Q LOSS MUTATED                                            2
  6Q LOSS WILD-TYPE                                          3
                   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                                               2
  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                                       6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             124
  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                    2
  MUCINOUS (COLLOID) CARCINOMA                                     2
                                                    clus
vv                                                   6Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               179
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  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    10 191
  6Q LOSS WILD-TYPE  11 264
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     10  191
  6Q LOSS WILD-TYPE   11  264
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               10                11
  YES             191               264
[1] 2 2
[1] FALSE
D52V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED   145   4   1   7
  6Q LOSS WILD-TYPE 182   8   3  14
D52V12, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0             145               182
  R1               4                 8
  R2               1                 3
  RX               7                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
  6Q LOSS MUTATED                                  0     2
  6Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                          13   159
  6Q LOSS WILD-TYPE                        22   208
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                     13                22
  WHITE                                        159               208
[1] 4 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     3 144
  6Q LOSS WILD-TYPE   4 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  144
  6Q LOSS WILD-TYPE    4  201
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 4
  NOT HISPANIC OR LATINO             144               201
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    24   6
  7P LOSS WILD-TYPE 305  81
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               30               386 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6                81 
$`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-95-A4VP TCGA-97-8174 
         492           36          186           34          605         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-49-AARQ TCGA-50-5045 
         369          890          522          354         6443         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-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         282         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         764          686         1015          255          105         1986 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
        1971          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-55-7284 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 
         705           39           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-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33          462          100            6          600 
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-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          66          674          216           44           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-55-8614 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-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V 
        1289         1970         2696         1445         2067         2199 
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-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
         866          610          573          427          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
         422          202          186          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-73-4662 TCGA-73-4666 
         129          214           61         1600          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-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 
         519          305         1970         1967         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-78-7152 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-78-7535 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-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
          10           14           39         1940           60          310 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
          79          417          842          224           35          505 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 
         174           44          218          297          127            2 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1973          568          377          477          476          830 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
          84          121          553          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-97-8175 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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
         435          116            6          266          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         102          827         1175           84         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 TCGA-S2-AA1A 
        1490          121 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                8                 1 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1965              6443 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            460.5             476.5 
[1] "8.0 - 1965.0 (460.5)" "1.0 - 6443.0 (476.5)"
[1] "hr=" "1.8"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  7P LOSS MUTATED         0        7        8         3         7          5
  7P LOSS WILD-TYPE       5      109      124        46        63         63
                   vv
clus                STAGE IIIB STAGE IV
  7P LOSS MUTATED            1        1
  7P LOSS WILD-TYPE         10       23
D53V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                 7               109
  STAGE IB                 8               124
  STAGE IIA                3                46
  STAGE IIB                7                63
  STAGE IIIA               5                63
  STAGE IIIB               1                10
  STAGE IV                 1                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
  7P LOSS MUTATED     8  20   3   1
  7P LOSS WILD-TYPE 139 247  39  17
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               8               139
  T2              20               247
  T3               3                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
  7P LOSS MUTATED    22   5     5
  7P LOSS WILD-TYPE 279  86    69
D53V5, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0                 22               279
  N1                  5                86
  N2+N3               5                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
  7P LOSS MUTATED    26   1   0   0   5
  7P LOSS WILD-TYPE 300  17   1   4 118
D53V6, multiclass
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               26               300
  M1                1                17
  M1A               0                 1
  M1B               0                 4
  MX                5               118
[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    15  17
  7P LOSS WILD-TYPE 240 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     15   17
  7P LOSS WILD-TYPE  240  204
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE              15               240
  MALE                17               204
[1] 2 2
[1] FALSE
D53V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7P LOSS MUTATED                            1
  7P LOSS WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7P LOSS MUTATED                                   4
  7P LOSS WILD-TYPE                                90
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                   22
  7P LOSS WILD-TYPE                                                281
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7P LOSS MUTATED                                            0
  7P LOSS WILD-TYPE                                          5
                   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                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  7P LOSS MUTATED                              1
  7P LOSS WILD-TYPE                            6
D53V9, multiclass
                                                    clus
vv                                                   7P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              22
  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                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      5
  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  30
  7P LOSS WILD-TYPE  19 425
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2   30
  7P LOSS WILD-TYPE   19  425
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                2                19
  YES              30               425
[1] 2 2
[1] FALSE
D53V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    18   1   0   2
  7P LOSS WILD-TYPE 309  11   4  19
D53V12, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              18               309
  R1               1                11
  R2               0                 4
  RX               2                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
  7P LOSS MUTATED                                  0     1
  7P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           1    27
  7P LOSS WILD-TYPE                        34   340
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                34
  WHITE                                         27               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"
D53V14, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  25
  7P LOSS WILD-TYPE   6 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   25
  7P LOSS WILD-TYPE    6  320
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              25               320
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    30   4
  7Q LOSS WILD-TYPE 299  83
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               34               382 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                83 
$`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-95-A4VP 
         323          372          492          186           34          605 
TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M7 TCGA-99-8032 
        1965          147          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-49-AARQ TCGA-50-5045 TCGA-50-5049 
         890          522          354         6443         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-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         280          701         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          705           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-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
          21            3           31            5           33          462 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
         100            6          600           26            4           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
          15           33           46           66          674          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-A492 TCGA-55-A493 TCGA-55-A494 
          42           29           48            1           28            5 
TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U 
          47         1216         1289         1970         2696         2067 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
        2199         1246          910         1728          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-67-3772 TCGA-67-3773 TCGA-67-6215 
         864         1559          866          573          427          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-69-8253 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-73-4670 TCGA-73-4675 
         711          912          800          467          131           40 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-7027 
         164           38          621          519          305         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
        1965         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-78-7159 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-86-6851 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-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-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         842          224           35          505          174           36 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7043 TCGA-95-7562 
          44          218          297          127            2         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
         568          377          477          476          830           84 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         121          553          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-97-8179 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-L9-A50W 
         238          578          435          116            6          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         312          111          102          827         1175           84 
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-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 TCGA-S2-AA1A 
        1955         1971         1490          121 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               31                 1 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1970              6443 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            465.5             476.5 
[1] "31.0 - 1970.0 (465.5)" "1.0 - 6443.0 (476.5)" 
[1] "hr=" "1.3"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  7Q LOSS MUTATED         0       11       11         2         7          6
  7Q LOSS WILD-TYPE       5      105      121        47        63         62
                   vv
clus                STAGE IIIB STAGE IV
  7Q LOSS MUTATED            1        0
  7Q LOSS WILD-TYPE         10       24
D54V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                11               105
  STAGE IB                11               121
  STAGE IIA                2                47
  STAGE IIB                7                63
  STAGE IIIA               6                62
  STAGE IIIB               1                10
  STAGE IV                 0                24
[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  21   3   1
  7Q LOSS WILD-TYPE 134 246  39  17
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              13               134
  T2              21               246
  T3               3                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
  7Q LOSS MUTATED    27   5     6
  7Q LOSS WILD-TYPE 274  86    68
D54V5, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0                 27               274
  N1                  5                86
  N2+N3               6                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
  7Q LOSS MUTATED    32   0   0   0   6
  7Q LOSS WILD-TYPE 294  18   1   4 117
D54V6, multiclass
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               32               294
  M1                0                18
  M1A               0                 1
  M1B               0                 4
  MX                6               117
[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    21  17
  7Q LOSS WILD-TYPE 234 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     21   17
  7Q LOSS WILD-TYPE  234  204
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              21               234
  MALE                17               204
[1] 2 2
[1] FALSE
D54V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  7Q LOSS MUTATED                            1
  7Q LOSS WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  7Q LOSS MUTATED                                   7
  7Q LOSS WILD-TYPE                                87
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                   25
  7Q LOSS WILD-TYPE                                                278
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  7Q LOSS MUTATED                                            0
  7Q LOSS WILD-TYPE                                          5
                   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                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  7Q LOSS MUTATED                              1
  7Q LOSS WILD-TYPE                            6
D54V9, multiclass
                                                    clus
vv                                                   7Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              25
  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                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               278
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      5
  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  37
  7Q LOSS WILD-TYPE  20 418
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   37
  7Q LOSS WILD-TYPE   20  418
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1                20
  YES              37               418
[1] 2 2
[1] FALSE
D54V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    24   1   0   2
  7Q LOSS WILD-TYPE 303  11   4  19
D54V12, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              24               303
  R1               1                11
  R2               0                 4
  RX               2                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
  7Q LOSS MUTATED                                  0     2
  7Q LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           2    27
  7Q LOSS WILD-TYPE                        33   340
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                33
  WHITE                                         27               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"
D54V14, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  27
  7Q LOSS WILD-TYPE   6 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   27
  7Q LOSS WILD-TYPE    6  318
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              27               318
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   130  32
  8P LOSS WILD-TYPE 199  55
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              162               254 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               32                55 
$`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-49-AARQ TCGA-50-5049 TCGA-50-5066 
         369          890          354         6443         2146          944 
TCGA-50-5068 TCGA-50-5931 TCGA-50-5932 TCGA-50-5941 TCGA-50-6597 TCGA-53-7624 
        1499          267         1091          567         1015         1986 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6980 
        1971          280         1178         1479           87           67 
TCGA-55-6985 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7726 
        1233           35            6            4           40           39 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8092 
          34           19            3           31            5           26 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 
          15           33           66           23           11          228 
TCGA-55-8616 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8402 
          48         1952           28          162         1216         1445 
TCGA-62-A46U TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 
        2067         1728         1189         1686         1968           62 
TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 
        1305          866           31          610          573          422 
TCGA-69-7760 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K 
         202           70           89          382          129          214 
TCGA-73-4662 TCGA-73-4668 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 
         912          467          621          519          305         1970 
TCGA-75-7025 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7536 TCGA-78-7542 
        1967         1963         1202         1957         1949         1952 
TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 TCGA-86-7713 TCGA-86-7953 
        1949         1954         1964         1959          422          591 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
        1963          745           10           24          479          482 
TCGA-86-8668 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6836 TCGA-91-6847 
          45           10           30           14          417          842 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
          36          218          186           34            2         1973 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
         377          477          830           84          121          553 
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-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         266          111          102         1175           84         1946 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TK 
        1967         1954         1954         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          705           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          462          100            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
         600            4           47           46          674          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 
          44           29            8           15            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-A48Z TCGA-55-A490 TCGA-55-A492 
         106           33           42           29           48            1 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46V 
           5           47         1289         1970         2696         2199 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 
        1246          910          628         1126         1959          864 
TCGA-64-5781 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 
        1559          427          385          174          141          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8253 
         690          414          165          230          184          100 
TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 
          77           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-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          19           26           35           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
         455          405           39          323         1940           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
         310           79          372          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 TCGA-95-7567 
         505          174           44          297          127          568 
TCGA-95-7948 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         476          605         1965         1932         1332           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-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG 
         197          427          459          170          287          238 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T2 
         435          116            6          312          827         1951 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1957         1951         1970         1970          142         1955 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                 1 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             6443              2696 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            484.0             460.5 
[1] "2.0 - 6443.0 (484.0)" "1.0 - 2696.0 (460.5)"
[1] "hr=" "1"  
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  8P LOSS MUTATED         3       46       51        22        31         24
  8P LOSS WILD-TYPE       2       70       81        27        39         44
                   vv
clus                STAGE IIIB STAGE IV
  8P LOSS MUTATED            3        8
  8P LOSS WILD-TYPE          8       16
D55V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                46                70
  STAGE IB                51                81
  STAGE IIA               22                27
  STAGE IIB               31                39
  STAGE IIIA              24                44
  STAGE IIIB               3                 8
  STAGE IV                 8                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    62 105  15   5
  8P LOSS WILD-TYPE  85 162  27  13
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              62                85
  T2             105               162
  T3              15                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   118  39    28
  8P LOSS WILD-TYPE 183  52    46
D55V5, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0                118               183
  N1                 39                52
  N2+N3              28                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  8P LOSS MUTATED   127   6   1   1  52
  8P LOSS WILD-TYPE 199  12   0   3  71
D55V6, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              127               199
  M1                6                12
  M1A               1                 0
  M1B               1                 3
  MX               52                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   111  77
  8P LOSS WILD-TYPE 144 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    111   77
  8P LOSS WILD-TYPE  144  144
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE             111               144
  MALE                77               144
[1] 2 2
[1] FALSE
D55V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8P LOSS MUTATED                            7
  8P LOSS WILD-TYPE                          8
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8P LOSS MUTATED                                  33
  8P LOSS WILD-TYPE                                61
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                  127
  8P LOSS WILD-TYPE                                                176
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8P LOSS MUTATED                                            1
  8P LOSS WILD-TYPE                                          4
                   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                                               3
  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                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             127
  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                    3
  MUCINOUS (COLLOID) CARCINOMA                                     0
                                                    clus
vv                                                   8P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               176
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  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     5 183
  8P LOSS WILD-TYPE  16 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5  183
  8P LOSS WILD-TYPE   16  272
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                5                16
  YES             183               272
[1] 2 2
[1] FALSE
D55V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   131   2   1  12
  8P LOSS WILD-TYPE 196  10   3   9
D55V12, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             131               196
  R1               2                10
  R2               1                 3
  RX              12                 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                          16   138
  8P LOSS WILD-TYPE                        19   229
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                     16                19
  WHITE                                        138               229
[1] 4 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     5 136
  8P LOSS WILD-TYPE   2 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5  136
  8P LOSS WILD-TYPE    2  209
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 2
  NOT HISPANIC OR LATINO             136               209
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    36   8
  8Q LOSS WILD-TYPE 293  79
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               44               372 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8                79 
$`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-73-A9RS TCGA-75-7025 TCGA-78-7150 TCGA-78-8640 
         467          621          305         1967         1963         1949 
TCGA-86-6851 TCGA-86-8055 TCGA-86-8074 TCGA-86-8279 TCGA-95-7039 TCGA-95-7944 
        1959           10           24          482           34          377 
TCGA-95-8494 TCGA-97-7546 TCGA-97-7554 TCGA-97-8171 TCGA-97-8547 TCGA-97-A4M7 
          84          964          775          107          148          271 
TCGA-MP-A4T7 TCGA-MP-A4TK 
        1954         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-49-AARQ TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 
         522          354         6443         2174          455          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
         944          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-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
         105         1986          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-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 
        2151         1170           18           35          121            6 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
          95           40          705           39           39           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-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33          462          100            6          600 
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-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          66          674          216           44           23           29 
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-62-8397 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-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 
        1246          910          628         1189         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-69-7764 TCGA-69-7765 
         141          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-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
         129          214           61         1600          711          800 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-6214 
         131           40          164           38          519         1970 
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-78-7154 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-78-7535 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-78-8648 TCGA-78-8655 
         327          881         1952          994         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-86-7953 TCGA-86-7954 TCGA-86-7955 
         630          422         1968          591         1963          508 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
         745         1963           13          479          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-86-8669 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          505          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 
         218          297          127          186            2         1973 
TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
         568          477          476          830          121          553 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 
         605         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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
         435          116            6          266          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         102          827         1175           84         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 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-A4TI TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970         1970          142         1955         1490          121 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                 1 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             2146              6443 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            606.5             464.0 
[1] "4.0 - 2146.0 (606.5)" "1.0 - 6443.0 (464.0)"
[1] "hr=" "1.5"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  8Q LOSS MUTATED         1       11        9        10         8          7
  8Q LOSS WILD-TYPE       4      105      123        39        62         61
                   vv
clus                STAGE IIIB STAGE IV
  8Q LOSS MUTATED            2        3
  8Q LOSS WILD-TYPE          9       21
D56V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  1                 4
  STAGE IA                11               105
  STAGE IB                 9               123
  STAGE IIA               10                39
  STAGE IIB                8                62
  STAGE IIIA               7                61
  STAGE IIIB               2                 9
  STAGE IV                 3                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
  8Q LOSS MUTATED    18  25   6   2
  8Q LOSS WILD-TYPE 129 242  36  16
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              18               129
  T2              25               242
  T3               6                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
  8Q LOSS MUTATED    26  14    10
  8Q LOSS WILD-TYPE 275  77    64
D56V5, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0                 26               275
  N1                 14                77
  N2+N3              10                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
  8Q LOSS MUTATED    35   2   1   0  13
  8Q LOSS WILD-TYPE 291  16   0   4 110
D56V6, multiclass
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               35               291
  M1                2                16
  M1A               1                 0
  M1B               0                 4
  MX               13               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"
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    31  20
  8Q LOSS WILD-TYPE 224 201
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     31   20
  8Q LOSS WILD-TYPE  224  201
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              31               224
  MALE                20               201
[1] 2 2
[1] FALSE
D56V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  8Q LOSS MUTATED                            1
  8Q LOSS WILD-TYPE                         14
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  8Q LOSS MUTATED                                   9
  8Q LOSS WILD-TYPE                                85
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                   33
  8Q LOSS WILD-TYPE                                                270
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  8Q LOSS MUTATED                                            0
  8Q LOSS WILD-TYPE                                          5
                   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                                             4
                   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)              33
  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                                        14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               270
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      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"
D56V10, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  50
  8Q LOSS WILD-TYPE  20 405
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   50
  8Q LOSS WILD-TYPE   20  405
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                1                20
  YES              50               405
[1] 2 2
[1] FALSE
D56V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    35   1   0   1
  8Q LOSS WILD-TYPE 292  11   4  20
D56V12, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              35               292
  R1               1                11
  R2               0                 4
  RX               1                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                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                           2    36
  8Q LOSS WILD-TYPE                        33   331
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                      2                33
  WHITE                                         36               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"
D56V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  36
  8Q LOSS WILD-TYPE   6 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   36
  8Q LOSS WILD-TYPE    6  309
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 6
  NOT HISPANIC OR LATINO              36               309
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   163  53
  9P LOSS WILD-TYPE 166  34
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              216               200 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               53                34 
$`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          705           39           16 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
           3           31          100            6          600           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-73-A9RS TCGA-75-6214 
         912          467          131           40          305         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
        1967         1956         1965         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-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7937 TCGA-97-8174 
         830           84          121          605          181         1965 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 
         147           15          148          115          271           44 
TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A7SV TCGA-L9-A8F4 
         170          154          287          238          111          102 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 
         827         1175           84         1946         1967         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 
        1957         1980         1951         1970         1970         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-49-AARQ TCGA-50-5045 
         157          890          522          354         6443         2174 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5941 TCGA-50-5942 TCGA-50-6597 
        2146          455          944          567          883         1015 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 
         280         1479            2         1239         1475         1826 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
        1170          121           95           39           34           24 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8085 
          54           19          197           21            5           33 
TCGA-55-8087 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
         462           47           33          674          216           44 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 
          23           11           15            9          146          202 
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-A491 TCGA-55-A494 TCGA-55-A4DF TCGA-62-A46U TCGA-64-1677 TCGA-64-5774 
        1952            5           47         2067          628         1959 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3773 TCGA-67-6215 
          62         1305          864         1559          427          174 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
         165          230           70           89          100           77 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4676 
         214           61         1600          711          800          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7145 TCGA-78-7152 TCGA-78-7153 
          38          621          519         1973         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 
        1948         1957         1963         1221         1940         1950 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-8648 TCGA-78-8662 
        1972         1949         1944          327         1971         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 
        1965         1972          824         1959           11         1968 
TCGA-86-7953 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8359 
         591           13          489          476         1955           26 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 
          34           18          455          405           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6836 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
          39          323          417          492          505          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
          44          218          297          186           34            2 
TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 
        1973          377          477          553          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-97-8175 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-J2-8194 
          87          197          392          427          459          114 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
         282          578          435          116            6          266 
TCGA-L9-A743 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI 
         312         1951         1954         1944          142         1955 
TCGA-MP-A4TK TCGA-S2-AA1A 
        1971          121 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                 2 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             2696              6443 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            535.5             455.0 
[1] "1.0 - 2696.0 (535.5)" "2.0 - 6443.0 (455.0)"
[1] "hr=" "1.2"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  9P LOSS MUTATED         3       54       63        28        39         40
  9P LOSS WILD-TYPE       2       62       69        21        31         28
                   vv
clus                STAGE IIIB STAGE IV
  9P LOSS MUTATED            6       12
  9P LOSS WILD-TYPE          5       12
D57V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                54                62
  STAGE IB                63                69
  STAGE IIA               28                21
  STAGE IIB               39                31
  STAGE IIIA              40                28
  STAGE IIIB               6                 5
  STAGE IV                12                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
  9P LOSS MUTATED    73 140  22   9
  9P LOSS WILD-TYPE  74 127  20   9
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              73                74
  T2             140               127
  T3              22                20
  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
  9P LOSS MUTATED   145  54    42
  9P LOSS WILD-TYPE 156  37    32
D57V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                145               156
  N1                 54                37
  N2+N3              42                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A M1B  MX
  9P LOSS MUTATED   172  10   0   2  59
  9P LOSS WILD-TYPE 154   8   1   2  64
D57V6, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              172               154
  M1               10                 8
  M1A               0                 1
  M1B               2                 2
  MX               59                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"
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   120 125
  9P LOSS WILD-TYPE 135  96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    120  125
  9P LOSS WILD-TYPE  135   96
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE             120               135
  MALE               125                96
[1] 2 2
[1] FALSE
D57V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9P LOSS MUTATED                            9
  9P LOSS WILD-TYPE                          6
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9P LOSS MUTATED                                  48
  9P LOSS WILD-TYPE                                46
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                  158
  9P LOSS WILD-TYPE                                                145
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9P LOSS MUTATED                                            2
  9P LOSS WILD-TYPE                                          3
                   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                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  9P LOSS MUTATED                              2
  9P LOSS WILD-TYPE                            5
D57V9, multiclass
                                                    clus
vv                                                   9P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             158
  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                                 46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               145
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         3
  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                      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"
D57V10, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    10 235
  9P LOSS WILD-TYPE  11 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     10  235
  9P LOSS WILD-TYPE   11  220
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               10                11
  YES             235               220
[1] 2 2
[1] FALSE
D57V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED   167   5   2  11
  9P LOSS WILD-TYPE 160   7   2  10
D57V12, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             167               160
  R1               5                 7
  R2               2                 2
  RX              11                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
  9P LOSS MUTATED                                  1     2
  9P LOSS WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          16   192
  9P LOSS WILD-TYPE                        19   175
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                     16                19
  WHITE                                        192               175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     4 172
  9P LOSS WILD-TYPE   3 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4  172
  9P LOSS WILD-TYPE    3  173
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             172               173
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   156  45
  9Q LOSS WILD-TYPE 173  42
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              201               215 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               45                42 
$`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          705           39           16           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8094 TCGA-55-8097 
           3           31          100            6            4           15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
          46           66           29            8           15          228 
TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48X TCGA-55-A491 
           3          202          536           15           33         1952 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 
           1           28            5           47          162         1289 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-64-1676 TCGA-64-1679 
        1970         2696         1445         2199         1728         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 
        1126         1968         1959          864           31          610 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         573          385          422          202          186          690 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 
         230          184          382          129          214          711 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-A9RS TCGA-75-6214 
         912          467          131           40          305         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-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7937 TCGA-97-8174 
         830           84          121          605          181         1965 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 
         147          148          115          271           44          170 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
         154          287          238          111          102          827 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1175         1946         1967         1954         1980         1951 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 
        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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
         354         6443         2174         2146          455          944 
TCGA-50-5930 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6597 TCGA-53-7626 
         282          567          883          686         1015         1971 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 TCGA-55-6969 TCGA-55-6972 TCGA-55-6983 
         280         1479            2         1239         1475         1826 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 
        1170          121           95           40           39           34 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 
          24           54           19          197            5           33 
TCGA-55-8087 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 
         462          600           26           47           33          674 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8511 TCGA-55-8513 
         216           44           23           11            9          146 
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-62-8395 TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 
          48         1216         2067         1246          910          628 
TCGA-64-1678 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 
        1189           62         1305         1559          866          427 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 
         174          141          414          165           70           89 
TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 TCGA-73-4666 TCGA-73-4676 
         100           77           61         1600          800          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7031 TCGA-78-7152 TCGA-78-7153 
          38          621          519         1965         1202          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 
        1948         1957         1961         1963          678         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
        1950         1934         1972         1949         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 
         881         1952         1971         1981         1964         1965 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 
         824         1959           11         1968          591          745 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 TCGA-86-8359 
        1963           13          489          476         1955           26 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 
          34           18          455          405           30           14 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6836 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
          39          323          417           35          492          505 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7043 
         174           44          218          297          186            2 
TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 
        1973          377          477          553          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-97-8175 TCGA-97-8179 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
          87           15          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-L9-A50W TCGA-L9-A743 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 
         266          312           84         1951         1954         1957 
TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-S2-AA1A 
        1944          142         1955         1971          121 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 2 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             2696              6443 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              479               466 
[1] "1.0 - 2696.0 (479.0)" "2.0 - 6443.0 (466.0)"
[1] "hr=" "1"  
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  9Q LOSS MUTATED         3       54       63        26        32         37
  9Q LOSS WILD-TYPE       2       62       69        23        38         31
                   vv
clus                STAGE IIIB STAGE IV
  9Q LOSS MUTATED            4       12
  9Q LOSS WILD-TYPE          7       12
D58V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  3                 2
  STAGE IA                54                62
  STAGE IB                63                69
  STAGE IIA               26                23
  STAGE IIB               32                38
  STAGE IIIA              37                31
  STAGE IIIB               4                 7
  STAGE IV                12                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
  9Q LOSS MUTATED    73 133  19   5
  9Q LOSS WILD-TYPE  74 134  23  13
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              73                74
  T2             133               134
  T3              19                23
  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   139  48    39
  9Q LOSS WILD-TYPE 162  43    35
D58V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                139               162
  N1                 48                43
  N2+N3              39                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
  9Q LOSS MUTATED   157  10   0   2  60
  9Q LOSS WILD-TYPE 169   8   1   2  63
D58V6, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              157               169
  M1               10                 8
  M1A               0                 1
  M1B               2                 2
  MX               60                63
[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   123 108
  9Q LOSS WILD-TYPE 132 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    123  108
  9Q LOSS WILD-TYPE  132  113
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE             123               132
  MALE               108               113
[1] 2 2
[1] FALSE
D58V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  9Q LOSS MUTATED                            8
  9Q LOSS WILD-TYPE                          7
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  9Q LOSS MUTATED                                  40
  9Q LOSS WILD-TYPE                                54
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                  153
  9Q LOSS WILD-TYPE                                                150
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  9Q LOSS MUTATED                                            1
  9Q LOSS WILD-TYPE                                          4
                   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                                             2
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  9Q LOSS MUTATED                              3
  9Q LOSS WILD-TYPE                            4
D58V9, multiclass
                                                    clus
vv                                                   9Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             153
  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                                 54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               150
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         4
  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                      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"
D58V10, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     9 222
  9Q LOSS WILD-TYPE  12 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9  222
  9Q LOSS WILD-TYPE   12  233
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                9                12
  YES             222               233
[1] 2 2
[1] FALSE
D58V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED   158   6   2  11
  9Q LOSS WILD-TYPE 169   6   2  10
D58V12, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0             158               169
  R1               6                 6
  R2               2                 2
  RX              11                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
  9Q LOSS MUTATED                                  1     2
  9Q LOSS WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          16   181
  9Q LOSS WILD-TYPE                        19   186
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                     16                19
  WHITE                                        181               186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     4 166
  9Q LOSS WILD-TYPE   3 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4  166
  9Q LOSS WILD-TYPE    3  179
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 3
  NOT HISPANIC OR LATINO             166               179
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    62  23
  10P LOSS WILD-TYPE 267  64
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                85                331 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                23                 64 
$`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-49-AARQ TCGA-50-5931 TCGA-50-5944 
        1421          428          445         6443          267          764 
TCGA-50-6597 TCGA-55-1596 TCGA-55-6980 TCGA-55-6986 TCGA-55-7281 TCGA-55-7994 
        1015         1375           67         2151           18           31 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8514 TCGA-55-8614 TCGA-55-A48X TCGA-55-A4DF 
         600            4          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-A59K 
          62          864           31          573          230          214 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-78-7147 TCGA-78-7540 TCGA-78-8640 
         711          800          467         1950          881         1949 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-8054 
        1981         1954          824         1959         1963          745 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 
          10           24          479          476           16           26 
TCGA-86-8669 TCGA-91-6828 TCGA-91-6835 TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 
          34          323           79          372           36          127 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-8494 TCGA-97-7546 TCGA-97-8547 
           2         1973          477           84          964          148 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-MP-A4T2 TCGA-MP-A4T4 
         271          154          287          238         1951         1954 
TCGA-MP-A4T9 
        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          705           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          462          100            6           26 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
          47           15           33           46           66          674 
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-55-8615 
          15          228            9            3          146           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-55-A494 TCGA-62-8395 
          48         1952            1           28            5         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-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5778 TCGA-64-5781 
         910          628         1189         1126         1305         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-69-7974 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-73-4662 TCGA-73-4670 TCGA-73-4675 
         129           61         1600          912          131           40 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 
         164           38          621          519          305         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-78-7149 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-78-7535 TCGA-78-7536 
        1950         1934         1937         1965         1972         1949 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8662 
        1944          327         1952          994         1971         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1965         1972           11          630          422         1968 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 
         591          508         1963           13          489          482 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
        1955           19           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-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
        1940           60          310          417          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
          35          492          505          174           44          218 
TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 
         297          186           34          568          377          476 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
         830          121          553          605         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-97-8552 TCGA-97-A4M2 
        1965           87          147           15          115          197 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
         392          427          459           44          170          114 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
         282          578          435          116            6          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         312          111          102          827         1175           84 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        1946         1967         1954         1957         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 
TCGA-S2-AA1A 
         121 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                  1 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              6443               2696 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               477                466 
[1] "2.0 - 6443.0 (477.0)" "1.0 - 2696.0 (466.0)"
[1] "hr=" "1.2"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  10P LOSS MUTATED         1       28       23        13        17         16
  10P LOSS WILD-TYPE       4       88      109        36        53         52
                    vv
clus                 STAGE IIIB STAGE IV
  10P LOSS MUTATED            1        5
  10P LOSS WILD-TYPE         10       19
D59V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 28                 88
  STAGE IB                 23                109
  STAGE IIA                13                 36
  STAGE IIB                17                 53
  STAGE IIIA               16                 52
  STAGE IIIB                1                 10
  STAGE IV                  5                 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
  10P LOSS MUTATED    39  54   8   2
  10P LOSS WILD-TYPE 108 213  34  16
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               39                108
  T2               54                213
  T3                8                 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
  10P LOSS MUTATED    60  25    17
  10P LOSS WILD-TYPE 241  66    57
D59V5, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                  60                241
  N1                  25                 66
  N2+N3               17                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  10P LOSS MUTATED    73   4   0   1  25
  10P LOSS WILD-TYPE 253  14   1   3  98
D59V6, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                73                253
  M1                 4                 14
  M1A                0                  1
  M1B                1                  3
  MX                25                 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"
D59V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    67  37
  10P LOSS WILD-TYPE 188 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     67   37
  10P LOSS WILD-TYPE  188  184
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               67                188
  MALE                 37                184
[1] 2 2
[1] FALSE
D59V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10P LOSS MUTATED                            4
  10P LOSS WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10P LOSS MUTATED                                  13
  10P LOSS WILD-TYPE                                81
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                   76
  10P LOSS WILD-TYPE                                                227
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10P LOSS MUTATED                                            1
  10P LOSS WILD-TYPE                                          4
                    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                                             4
                    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)               76
  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                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                227
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  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                       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"
D59V10, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2 102
  10P LOSS WILD-TYPE  19 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2  102
  10P LOSS WILD-TYPE   19  353
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 2                 19
  YES              102                353
[1] 2 2
[1] FALSE
D59V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    79   1   1   5
  10P LOSS WILD-TYPE 248  11   3  16
D59V12, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               79                248
  R1                1                 11
  R2                1                  3
  RX                5                 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
  10P LOSS MUTATED                                  1     1
  10P LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                           5    84
  10P LOSS WILD-TYPE                        30   283
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                       5                 30
  WHITE                                          84                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"
D59V14, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     2  79
  10P LOSS WILD-TYPE   5 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2   79
  10P LOSS WILD-TYPE    5  266
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               79                266
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    78  25
  10Q LOSS WILD-TYPE 251  62
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               103                313 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                25                 62 
$`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-49-AARQ 
         882           76         1081          428          445         6443 
TCGA-50-5931 TCGA-50-5944 TCGA-50-6597 TCGA-55-1596 TCGA-55-5899 TCGA-55-6971 
         267          764         1015         1375           87           25 
TCGA-55-6980 TCGA-55-6986 TCGA-55-7281 TCGA-55-7994 TCGA-55-8091 TCGA-55-8206 
          67         2151           18           31          600           46 
TCGA-55-8207 TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-A48X 
          66           29           15          202          536           33 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8402 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
          47          162         1445         1728         1686         1968 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 TCGA-69-7973 
        1959           62          864           31          573          230 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4668 
          70           89          129          214          800          467 
TCGA-73-A9RS TCGA-78-7147 TCGA-78-7535 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
         305         1950         1972          881         1952         1949 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-7955 
        1981         1954          824         1959         1963          508 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 
          10           24          479          476           16           26 
TCGA-86-8669 TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
          34          323         1940           79          372          842 
TCGA-91-8499 TCGA-93-7348 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
          36          127            2         1973          377          477 
TCGA-95-7948 TCGA-97-7546 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M7 TCGA-J2-8192 
         476          964           87          148          271          154 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A443 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 
         287          238          116         1951         1954         1980 
TCGA-MP-A4TF 
        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          705           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          462          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-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
         674          216           44           23           11            8 
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-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
         382          100           77           61         1600          711 
TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         912          131           40          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-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        1988         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-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8648 TCGA-78-8662 
        1949         1944          327          994         1971         1964 
TCGA-80-5607 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
        1965         1972           11          630          422         1968 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 
         591          745         1963           13          489          482 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
        1955           19           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-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
          60          310          417          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 
         505          174           44          218          297          186 
TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
          34          568          830           84          121          553 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         605         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-97-8552 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-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 
         170          114          282          578          435            6 
TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
         266          312          111          102          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA 
          84         1946         1967         1954         1957         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
        1944         1970          142         1955         1971         1490 
TCGA-S2-AA1A 
         121 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                  1 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              6443               2696 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               476                482 
[1] "2.0 - 6443.0 (476.0)" "1.0 - 2696.0 (482.0)"
[1] "hr=" "1"  
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  10Q LOSS MUTATED         1       33       35        14        21         15
  10Q LOSS WILD-TYPE       4       83       97        35        49         53
                    vv
clus                 STAGE IIIB STAGE IV
  10Q LOSS MUTATED            1        4
  10Q LOSS WILD-TYPE         10       20
D60V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 33                 83
  STAGE IB                 35                 97
  STAGE IIA                14                 35
  STAGE IIB                21                 49
  STAGE IIIA               15                 53
  STAGE IIIB                1                 10
  STAGE IV                  4                 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
  10Q LOSS MUTATED    44  68   9   2
  10Q LOSS WILD-TYPE 103 199  33  16
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               44                103
  T2               68                199
  T3                9                 33
  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    77  29    16
  10Q LOSS WILD-TYPE 224  62    58
D60V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                  77                224
  N1                  29                 62
  N2+N3               16                 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
  10Q LOSS MUTATED    88   4   0   0  32
  10Q LOSS WILD-TYPE 238  14   1   4  91
D60V6, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                88                238
  M1                 4                 14
  M1A                0                  1
  M1B                0                  4
  MX                32                 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"
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    74  50
  10Q LOSS WILD-TYPE 181 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     74   50
  10Q LOSS WILD-TYPE  181  171
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               74                181
  MALE                 50                171
[1] 2 2
[1] FALSE
D60V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  10Q LOSS MUTATED                            5
  10Q LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  10Q LOSS MUTATED                                  18
  10Q LOSS WILD-TYPE                                76
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                   86
  10Q LOSS WILD-TYPE                                                217
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  10Q LOSS MUTATED                                            1
  10Q LOSS WILD-TYPE                                          4
                    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                                             2
                    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)               86
  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                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  76
  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                                  1
  LUNG MUCINOUS ADENOCARCINOMA                                        2
  LUNG PAPILLARY ADENOCARCINOMA                                      19
  LUNG SIGNET RING ADENOCARCINOMA                                     0
  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"
D60V10, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     2 122
  10Q LOSS WILD-TYPE  19 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2  122
  10Q LOSS WILD-TYPE   19  333
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 2                 19
  YES              122                333
[1] 2 2
[1] FALSE
D60V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    91   1   1   7
  10Q LOSS WILD-TYPE 236  11   3  14
D60V12, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               91                236
  R1                1                 11
  R2                1                  3
  RX                7                 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 LOSS MUTATED                                  1     1
  10Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                           7    97
  10Q LOSS WILD-TYPE                        28   270
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                       7                 28
  WHITE                                          97                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"
D60V14, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3  89
  10Q LOSS WILD-TYPE   4 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3   89
  10Q LOSS WILD-TYPE    4  256
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               89                256
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    75  20
  11P LOSS WILD-TYPE 254  67
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                95                321 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                20                 67 
$`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-55-5899 
         267         1986         1971          280         1479           87 
TCGA-55-6642 TCGA-55-6972 TCGA-55-7570 TCGA-55-7573 TCGA-55-7727 TCGA-55-7815 
         993         1475            6            4           34           54 
TCGA-55-7903 TCGA-55-7994 TCGA-55-8089 TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 
          19           31          100           23            8          228 
TCGA-55-8511 TCGA-55-8615 TCGA-55-A490 TCGA-55-A492 TCGA-55-A4DG TCGA-62-8397 
           9           15           48            1          162         1289 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-5774 TCGA-64-5778 
        1246          910         1728         1686         1959         1305 
TCGA-64-5815 TCGA-69-7763 TCGA-69-7764 TCGA-69-A59K TCGA-73-4659 TCGA-73-4670 
         866          690          414          214          711          131 
TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-7025 TCGA-78-7145 TCGA-78-7148 
          40          519          305         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-95-8039 TCGA-95-8494 
         417          842          186          476          830           84 
TCGA-97-7553 TCGA-97-8174 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 
        1332         1965          287          578          111          102 
TCGA-MN-A4N1 TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TF 
         827         1951         1957         1970         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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         522          354         6443         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-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
         653          567          883          764          686         1015 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
         255          105          424          701         1178         1375 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 
           2           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-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
          95           40          705           39           39           24 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
          16          197           21            3            5           33 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
         462            6          600           26            4           47 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
          15           33           46           66          674          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
          44           29           11           15            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-A491 TCGA-55-A493 TCGA-55-A494 
          33           42           29         1952           28            5 
TCGA-55-A4DF TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U 
          47         1216         1970         2696         1445         2067 
TCGA-62-A46V TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
        2199          628         1189         1126         1968           62 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
         864         1559           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-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         165          230          184           70           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 
         100           77          129           61         1600          912 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 
         800          467          164           38          621         1970 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
        1956         1965         1988         1950         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-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
         215         1940         1950         1934         1937         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-78-8648 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-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         824         1959         1968         1963          508          745 
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-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         372          224           35          492          505          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 
          36           44          218          297          127           34 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK 
           2         1973          568          377          477          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 
         553          605          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-L9-A50W 
         282          238          435          116            6          266 
TCGA-L9-A743 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
         312         1175           84         1946         1967         1954 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI 
        1954         1980         1951         1944          142         1955 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1971         1490          121 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  2 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1986               6443 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               591                457 
[1] "1.0 - 1986.0 (591.0)" "2.0 - 6443.0 (457.0)"
[1] "hr=" "1.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  11P LOSS MUTATED         1       23       29        15        18         15
  11P LOSS WILD-TYPE       4       93      103        34        52         53
                    vv
clus                 STAGE IIIB STAGE IV
  11P LOSS MUTATED            0        7
  11P LOSS WILD-TYPE         11       17
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 23                 93
  STAGE IB                 29                103
  STAGE IIA                15                 34
  STAGE IIB                18                 52
  STAGE IIIA               15                 53
  STAGE IIIB                0                 11
  STAGE IV                  7                 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
  11P LOSS MUTATED    31  60  14   3
  11P LOSS WILD-TYPE 116 207  28  15
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               31                116
  T2               60                207
  T3               14                 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
  11P LOSS MUTATED    69  25    14
  11P LOSS WILD-TYPE 232  66    60
D61V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                  69                232
  N1                  25                 66
  N2+N3               14                 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
  11P LOSS MUTATED    74   7   0   0  27
  11P LOSS WILD-TYPE 252  11   1   4  96
D61V6, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                74                252
  M1                 7                 11
  M1A                0                  1
  M1B                0                  4
  MX                27                 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"
D61V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    41  67
  11P LOSS WILD-TYPE 214 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     41   67
  11P LOSS WILD-TYPE  214  154
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               41                214
  MALE                 67                154
[1] 2 2
[1] FALSE
D61V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11P LOSS MUTATED                            2
  11P LOSS WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11P LOSS MUTATED                                  21
  11P LOSS WILD-TYPE                                73
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                   78
  11P LOSS WILD-TYPE                                                225
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11P LOSS MUTATED                                            0
  11P LOSS WILD-TYPE                                          5
                    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                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  11P LOSS MUTATED                              1
  11P LOSS WILD-TYPE                            6
D61V9, multiclass
                                                    clus
vv                                                   11P LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               78
  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                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                225
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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                       5
  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     3 105
  11P LOSS WILD-TYPE  18 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3  105
  11P LOSS WILD-TYPE   18  350
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 3                 18
  YES              105                350
[1] 2 2
[1] FALSE
D61V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    75   2   1   8
  11P LOSS WILD-TYPE 252  10   3  13
D61V12, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               75                252
  R1                2                 10
  R2                1                  3
  RX                8                 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
  11P LOSS MUTATED                                  0     2
  11P LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                          11    81
  11P LOSS WILD-TYPE                        24   286
D61V13, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  4
  BLACK OR AFRICAN AMERICAN                      11                 24
  WHITE                                          81                286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     3  82
  11P LOSS WILD-TYPE   4 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3   82
  11P LOSS WILD-TYPE    4  263
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               82                263
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    62  14
  11Q LOSS WILD-TYPE 267  73
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                76                340 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                14                 73 
$`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-95-8039 
          19           34           30          842          186          830 
TCGA-95-8494 TCGA-95-A4VN TCGA-97-8174 TCGA-J2-A4AD TCGA-MN-A4N1 TCGA-MN-A4N5 
          84          553         1965          287          827           84 
TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TF 
        1951         1957         1970         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-49-AARQ 
         445          369          890          522          354         6443 
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-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         282         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         764          686         1015          255          105         1986 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
         424          280          701         1178         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          705 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          39           39           24           16          197           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
           3           31           33          462            6          600 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
          26           47           15           33           46           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
         674          216           44           29           11           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-A48Z 
          49           66          106           33           42           29 
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-64-1677 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 
        1246          628         1126         1968           62          864 
TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
        1559           31          610          573          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-69-7978 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-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         800          467          131          164           38          621 
TCGA-73-A9RS TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
         305         1956         1965         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-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        1963         1221          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-78-8648 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-86-7711 
        1964         1965         1972          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-86-8075 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-91-6836 TCGA-91-6840 TCGA-91-6848 
          60          310           79          417          372          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          35          492          505          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
         218          297          127           34            2         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP 
         568          377          477          476          121          605 
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-A4AE 
         459           44          170          154          114          282 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
         238          578          435          116            6          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
         312          111          102         1175         1946         1967 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH 
        1954         1954         1980         1951         1944          142 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1955         1971         1490          121 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                  1 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              1973               6443 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             684.0              451.5 
[1] "4.0 - 1973.0 (684.0)" "1.0 - 6443.0 (451.5)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  11Q LOSS MUTATED         0       20       22        14        13         13
  11Q LOSS WILD-TYPE       5       96      110        35        57         55
                    vv
clus                 STAGE IIIB STAGE IV
  11Q LOSS MUTATED            0        4
  11Q LOSS WILD-TYPE         11       20
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 20                 96
  STAGE IB                 22                110
  STAGE IIA                14                 35
  STAGE IIB                13                 57
  STAGE IIIA               13                 55
  STAGE IIIB                0                 11
  STAGE IV                  4                 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
  11Q LOSS MUTATED    27  49   8   2
  11Q LOSS WILD-TYPE 120 218  34  16
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               27                120
  T2               49                218
  T3                8                 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
  11Q LOSS MUTATED    56  17    13
  11Q LOSS WILD-TYPE 245  74    61
D62V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                  56                245
  N1                  17                 74
  N2+N3               13                 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
  11Q LOSS MUTATED    67   3   0   1  15
  11Q LOSS WILD-TYPE 259  15   1   3 108
D62V6, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                67                259
  M1                 3                 15
  M1A                0                  1
  M1B                1                  3
  MX                15                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"
D62V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    33  53
  11Q LOSS WILD-TYPE 222 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     33   53
  11Q LOSS WILD-TYPE  222  168
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               33                222
  MALE                 53                168
[1] 2 2
[1] FALSE
D62V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  11Q LOSS MUTATED                            3
  11Q LOSS WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  11Q LOSS MUTATED                                  16
  11Q LOSS WILD-TYPE                                78
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                   60
  11Q LOSS WILD-TYPE                                                243
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  11Q LOSS MUTATED                                            0
  11Q LOSS WILD-TYPE                                          5
                    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                                               1
  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                                        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                16
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               60
  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                     1
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   11Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                243
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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  84
  11Q LOSS WILD-TYPE  19 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   84
  11Q LOSS WILD-TYPE   19  371
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 2                 19
  YES               84                371
[1] 2 2
[1] FALSE
D62V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    63   2   0   6
  11Q LOSS WILD-TYPE 264  10   4  15
D62V12, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               63                264
  R1                2                 10
  R2                0                  4
  RX                6                 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 LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           5    66
  11Q LOSS WILD-TYPE                        30   301
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                 30
  WHITE                                          66                301
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0  67
  11Q LOSS WILD-TYPE   7 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   67
  11Q LOSS WILD-TYPE    7  278
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  7
  NOT HISPANIC OR LATINO               67                278
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    72  14
  12P LOSS WILD-TYPE 257  73
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                86                330 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                14                 73 
$`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-49-AARQ TCGA-50-5049 TCGA-50-5051 
         896          369          890         6443         2146          455 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5942 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 
        1499         1091          883          686         1015          701 
TCGA-55-5899 TCGA-55-7573 TCGA-55-7727 TCGA-55-7914 TCGA-55-8087 TCGA-55-8510 
          87            4           34            3          462          228 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-A48X 
           9          202          536           48           49           33 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A4DG TCGA-64-1676 TCGA-64-5778 TCGA-67-3771 
          29         1952          162         1728         1305          610 
TCGA-67-6217 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-8253 TCGA-71-6725 
         422          690          165          184          100           61 
TCGA-73-4677 TCGA-73-7498 TCGA-75-6214 TCGA-78-7147 TCGA-78-7153 TCGA-78-7535 
          38          621         1970         1950          760         1972 
TCGA-86-7701 TCGA-86-7955 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
          11          508           13           24          479          482 
TCGA-86-8358 TCGA-86-8672 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-95-7039 
          19           15          842           35          492           34 
TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 
           2          477          476          964         1965          775 
TCGA-97-8177 TCGA-99-7458 TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A7SV TCGA-L9-A8F4 
         147          392          427          287          111          102 
TCGA-MP-A4TC TCGA-MP-A4TK 
        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          705           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 
         600           26            4           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          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-A492 
          15           66          106           42           48            1 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
          28            5           47         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-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
         628         1189         1686         1126         1968         1959 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 
          62          864         1559          866           31          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
         427          385          174          141          202          186 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
         414          230           70           89          382           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-73-4676 TCGA-73-7499 TCGA-73-A9RS 
         467          131           40          164          519          305 
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-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 
         630          422         1968          591         1963          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-86-8359 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-91-6848 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         224          505          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
         297          127          186         1973          568          377 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 
         830           84          121          553          605         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-L9-A50W 
         238          578          435          116            6          266 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         312          827         1175           84         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-A5C7 TCGA-S2-AA1A 
        1970         1970          142         1955         1490          121 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                  1 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              6443               2696 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             458.5              487.5 
[1] "2.0 - 6443.0 (458.5)" "1.0 - 2696.0 (487.5)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  12P LOSS MUTATED         1       21       39         7        15         14
  12P LOSS WILD-TYPE       4       95       93        42        55         54
                    vv
clus                 STAGE IIIB STAGE IV
  12P LOSS MUTATED            1        4
  12P LOSS WILD-TYPE         10       20
D63V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 21                 95
  STAGE IB                 39                 93
  STAGE IIA                 7                 42
  STAGE IIB                15                 55
  STAGE IIIA               14                 54
  STAGE IIIB                1                 10
  STAGE IV                  4                 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
  12P LOSS MUTATED    26  65   7   3
  12P LOSS WILD-TYPE 121 202  35  15
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               26                121
  T2               65                202
  T3                7                 35
  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    67  20    14
  12P LOSS WILD-TYPE 234  71    60
D63V5, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                  67                234
  N1                  20                 71
  N2+N3               14                 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
  12P LOSS MUTATED    61   3   0   0  37
  12P LOSS WILD-TYPE 265  15   1   4  86
D63V6, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                61                265
  M1                 3                 15
  M1A                0                  1
  M1B                0                  4
  MX                37                 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"
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    65  37
  12P LOSS WILD-TYPE 190 184
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     65   37
  12P LOSS WILD-TYPE  190  184
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               65                190
  MALE                 37                184
[1] 2 2
[1] FALSE
D63V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12P LOSS MUTATED                            1
  12P LOSS WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12P LOSS MUTATED                                  20
  12P LOSS WILD-TYPE                                74
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                   69
  12P LOSS WILD-TYPE                                                234
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12P LOSS MUTATED                                            0
  12P LOSS WILD-TYPE                                          5
                    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                                             4
                    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)               69
  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                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                234
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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                       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"
D63V10, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3  99
  12P LOSS WILD-TYPE  18 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3   99
  12P LOSS WILD-TYPE   18  356
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 3                 18
  YES               99                356
[1] 2 2
[1] FALSE
D63V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    65   1   1   4
  12P LOSS WILD-TYPE 262  11   3  17
D63V12, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               65                262
  R1                1                 11
  R2                1                  3
  RX                4                 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
  12P LOSS MUTATED                                  0     1
  12P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                          13    80
  12P LOSS WILD-TYPE                        22   287
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                      13                 22
  WHITE                                          80                287
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2  83
  12P LOSS WILD-TYPE   5 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   83
  12P LOSS WILD-TYPE    5  262
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               83                262
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    60  15
  12Q LOSS WILD-TYPE 269  72
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                75                341 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                 72 
$`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-49-AARQ 
          76         1421          896          369          890         6443 
TCGA-50-5049 TCGA-50-5068 TCGA-50-5932 TCGA-50-5946 TCGA-50-6597 TCGA-55-1592 
        2146         1499         1091          686         1015          701 
TCGA-55-6980 TCGA-55-7283 TCGA-55-7727 TCGA-55-7914 TCGA-55-8510 TCGA-55-8511 
          67           35           34            3          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-A4DG TCGA-62-A46U TCGA-64-5778 TCGA-67-6217 TCGA-69-7763 TCGA-69-7765 
         162         2067         1305          422          690          165 
TCGA-69-7974 TCGA-69-8253 TCGA-71-6725 TCGA-73-4658 TCGA-73-4677 TCGA-73-7498 
         184          100           61         1600           38          621 
TCGA-75-6214 TCGA-78-7147 TCGA-78-7153 TCGA-78-7535 TCGA-86-7955 TCGA-86-8074 
        1970         1950          760         1972          508           24 
TCGA-86-8075 TCGA-86-8280 TCGA-91-6829 TCGA-91-6847 TCGA-91-7771 TCGA-95-7039 
         479           16         1940          842          492           34 
TCGA-95-7043 TCGA-95-7948 TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 
           2          476          830          964         1965          775 
TCGA-97-8177 TCGA-99-7458 TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A8F4 TCGA-MN-A4N1 
         147          392          427          287          102          827 
TCGA-MN-A4N5 TCGA-MP-A4TC TCGA-MP-A4TK 
          84         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          705           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          462          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
           6          600           26            4           47           15 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          33           46           66          674          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 
          23           29           11            8           15            3 
TCGA-55-8513 TCGA-55-8615 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 
         146           15           66          106           42           48 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 
        1952            1           28            5           47         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A471 
        1289         1970         2696         1445         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-64-5779 TCGA-64-5781 TCGA-64-5815 
        1968         1959           62          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-69-7764 TCGA-69-7973 TCGA-69-7978 
         141          202          186          414          230           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-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
         912          800          467          131           40          164 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         519          305         1967         1956         1965         1973 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
        1988         1944         1093         1963         1202         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-78-7540 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-86-7713 TCGA-86-7714 
         824         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-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         489          476          482         1955           19           26 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
          35           45           34           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-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 
          60          310           79          417          372          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
          35          505          174           36           44          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
         297          127          186         1973          568          377 
TCGA-95-7947 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 
         477           84          121          553          605         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-L9-A50W 
         238          578          435          116            6          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         312          111         1175         1946         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE 
        1954         1954         1957         1980         1951         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970          142         1955         1490          121 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                  1 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              6443               2696 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               492                466 
[1] "2.0 - 6443.0 (492.0)" "1.0 - 2696.0 (466.0)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  12Q LOSS MUTATED         1       16       32         8        15         14
  12Q LOSS WILD-TYPE       4      100      100        41        55         54
                    vv
clus                 STAGE IIIB STAGE IV
  12Q LOSS MUTATED            1        4
  12Q LOSS WILD-TYPE         10       20
D64V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 16                100
  STAGE IB                 32                100
  STAGE IIA                 8                 41
  STAGE IIB                15                 55
  STAGE IIIA               14                 54
  STAGE IIIB                1                 10
  STAGE IV                  4                 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
  12Q LOSS MUTATED    22  58   7   3
  12Q LOSS WILD-TYPE 125 209  35  15
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               22                125
  T2               58                209
  T3                7                 35
  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    55  21    14
  12Q LOSS WILD-TYPE 246  70    60
D64V5, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0                  55                246
  N1                  21                 70
  N2+N3               14                 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
  12Q LOSS MUTATED    52   3   0   0  35
  12Q LOSS WILD-TYPE 274  15   1   4  88
D64V6, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                52                274
  M1                 3                 15
  M1A                0                  1
  M1B                0                  4
  MX                35                 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"
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    60  31
  12Q LOSS WILD-TYPE 195 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     60   31
  12Q LOSS WILD-TYPE  195  190
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               60                195
  MALE                 31                190
[1] 2 2
[1] FALSE
D64V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  12Q LOSS MUTATED                            2
  12Q LOSS WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  12Q LOSS MUTATED                                  21
  12Q LOSS WILD-TYPE                                73
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                   54
  12Q LOSS WILD-TYPE                                                249
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  12Q LOSS MUTATED                                            0
  12Q LOSS WILD-TYPE                                          5
                    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                                             4
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  12Q LOSS MUTATED                              1
  12Q LOSS WILD-TYPE                            6
D64V9, multiclass
                                                    clus
vv                                                   12Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                21
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               54
  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                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                249
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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                       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"
D64V10, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2  89
  12Q LOSS WILD-TYPE  19 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   89
  12Q LOSS WILD-TYPE   19  366
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 2                 19
  YES               89                366
[1] 2 2
[1] FALSE
D64V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    56   1   1   5
  12Q LOSS WILD-TYPE 271  11   3  16
D64V12, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               56                271
  R1                1                 11
  R2                1                  3
  RX                5                 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                          12    71
  12Q LOSS WILD-TYPE                        23   296
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                      12                 23
  WHITE                                          71                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"
D64V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  73
  12Q LOSS WILD-TYPE   6 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   73
  12Q LOSS WILD-TYPE    6  272
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               73                272
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   160  42
  13Q LOSS WILD-TYPE 169  45
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               202                214 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                42                 45 
$`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          705           54           19 
TCGA-55-7911 TCGA-55-7994 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8207 
          21           31            6          600            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-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7539 TCGA-78-8640 
        1948         1957          678          215          327         1949 
TCGA-78-8660 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
        1954          824           11          630          422          591 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 
        1963          745           10          479          482           16 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-A456 TCGA-86-A4D0 
          19           26           45           34           10           30 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
         323         1940          310           79          417          372 
TCGA-91-8499 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7948 
          36          186           34         1973          568          476 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 
         830           84          553          605          964          775 
TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 
        1965          147          148          115          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-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A743 
         287          282          238          578          116          312 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 
         111          102         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-49-AARQ TCGA-50-5049 TCGA-50-5055 
        1700          445          522         6443         2146          785 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5932 TCGA-50-5942 TCGA-53-7624 TCGA-53-7626 
         944          246         1091          883         1986         1971 
TCGA-55-1592 TCGA-55-1594 TCGA-55-6543 TCGA-55-6969 TCGA-55-6983 TCGA-55-7281 
         701         1178            2         1239         1826           18 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
          35          121           95           39           39           34 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
          24           16          197            3            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
         462          100           26           47           15           33 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 TCGA-55-8512 
          46          674          216           29           11            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-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 
          48            1            5           47         1970         1445 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-67-3771 
        1189         1126         1959           62         1305          610 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 
         573          427          385          174          141          690 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-73-4666 
         230          184          382          100           77          800 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-75-6214 
         131          164           38          621          305         1970 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
        1967         1956         1950         1944         1093         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 
        1202          760         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-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
        1944          881         1952          994         1971         1981 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-86-6851 TCGA-86-7714 TCGA-86-7955 
        1964         1965         1972         1959         1968          508 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 
        1963           13           24          489          476         1955 
TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 
          35           18           15          455          405           14 
TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
          39           60          842          224           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         505          174           44          218          297          127 
TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 
           2          377          477          121         1965         1932 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
        1332          181           22          107          182           87 
TCGA-97-8179 TCGA-97-A4M7 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-MN-A4N1 
          15          271          435            6          266          827 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA 
        1175           84         1967         1954         1957         1951 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970          142         1490          121 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 4                  1 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              2696               6443 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               463                483 
[1] "4.0 - 2696.0 (463.0)" "1.0 - 6443.0 (483.0)"
[1] "hr=" "1"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  13Q LOSS MUTATED         3       49       63        25        39         34
  13Q LOSS WILD-TYPE       2       67       69        24        31         34
                    vv
clus                 STAGE IIIB STAGE IV
  13Q LOSS MUTATED            6       10
  13Q LOSS WILD-TYPE          5       14
D65V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 49                 67
  STAGE IB                 63                 69
  STAGE IIA                25                 24
  STAGE IIB                39                 31
  STAGE IIIA               34                 34
  STAGE IIIB                6                  5
  STAGE IV                 10                 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
  13Q LOSS MUTATED    62 136  21   9
  13Q LOSS WILD-TYPE  85 131  21   9
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               62                 85
  T2              136                131
  T3               21                 21
  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   138  50    37
  13Q LOSS WILD-TYPE 163  41    37
D65V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                 138                163
  N1                  50                 41
  N2+N3               37                 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
  13Q LOSS MUTATED   151   8   0   1  67
  13Q LOSS WILD-TYPE 175  10   1   3  56
D65V6, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               151                175
  M1                 8                 10
  M1A                0                  1
  M1B                1                  3
  MX                67                 56
[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   123 106
  13Q LOSS WILD-TYPE 132 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    123  106
  13Q LOSS WILD-TYPE  132  115
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE              123                132
  MALE                106                115
[1] 2 2
[1] FALSE
D65V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  13Q LOSS MUTATED                           11
  13Q LOSS WILD-TYPE                          4
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  13Q LOSS MUTATED                                  45
  13Q LOSS WILD-TYPE                                49
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                  147
  13Q LOSS WILD-TYPE                                                156
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  13Q LOSS MUTATED                                            1
  13Q LOSS WILD-TYPE                                          4
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  13Q LOSS MUTATED                                               8
  13Q LOSS WILD-TYPE                                            11
                    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                                               3
  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                                       11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              147
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                     8
  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                     3
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   13Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                156
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      11
  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     8 221
  13Q LOSS WILD-TYPE  13 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8  221
  13Q LOSS WILD-TYPE   13  234
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 8                 13
  YES              221                234
[1] 2 2
[1] FALSE
D65V11, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED   155   7   2  11
  13Q LOSS WILD-TYPE 172   5   2  10
D65V12, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0              155                172
  R1                7                  5
  R2                2                  2
  RX               11                 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                          20   173
  13Q LOSS WILD-TYPE                        15   194
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                      20                 15
  WHITE                                         173                194
[1] 4 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     4 169
  13Q LOSS WILD-TYPE   3 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4  169
  13Q LOSS WILD-TYPE    3  176
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              169                176
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    78  20
  14Q LOSS WILD-TYPE 251  67
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                98                318 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                20                 67 
$`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-73-A9RS TCGA-75-6214 
         382          214          912           40          305         1970 
TCGA-75-7027 TCGA-78-7146 TCGA-78-7150 TCGA-78-7535 TCGA-78-8640 TCGA-86-7711 
        1956         1988         1963         1972         1949          630 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8279 
         422          591         1963          745         1963          482 
TCGA-86-8359 TCGA-86-8669 TCGA-86-8672 TCGA-91-6830 TCGA-91-6848 TCGA-93-7347 
          26           34           15           60          224          297 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VN 
          34          568          377          476           84          553 
TCGA-97-7547 TCGA-97-8174 TCGA-97-8177 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 
        1965         1965          147          427           44          170 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4T7 
         287          238          312          827         1967         1954 
TCGA-MP-A4T8 TCGA-MP-A4TC 
        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-49-AARQ 
         157          369          890          522          354         6443 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
        2174         2146          455          785          944          246 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 
         282         1091         2370          653          567          883 
TCGA-50-5944 TCGA-50-5946 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
         764          686          255          105         1986         1971 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
         424          280         1178           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-55-7284 TCGA-55-7570 TCGA-55-7573 
        1233         2151         1170          121            6            4 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
          95           40          705           39           39           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-55-8090 
          31            5           33          462          100            6 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
         600           47           33           46           66          674 
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-55-8614 TCGA-55-8615 TCGA-55-8616 
           9            3          146          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-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
          48           28            5           47          162         1216 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 
        1289         2696         1445         2199          910         1728 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
         628         1189         1686         1968         1959           62 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
         866           31          610          573          427          174 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 
         141          202          690          414          230          184 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 
          70           89          100           77          129           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
        1600          711          800          467          131          164 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 
          38          621          519         1967         1965         1973 
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-78-7159 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-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
        1944          327          881         1952          994         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-86-7714 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 
        1959           11         1968          508           10           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 
          24          479          489          476           16         1955 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
          19           35           45           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-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
         310           79          417          372          842           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         492          505          174           36           44          218 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-8039 
         127          186            2         1973          477          830 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
         121          605          964         1932         1332          775 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 
         181           22          107          182           87           15 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 
         148          115          197          271          392          459 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         154          114          282          578          435          116 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
           6          266          111          102         1175           84 
TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE 
        1946         1951         1954         1980         1951         1970 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970          142         1955         1971         1490          121 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                  2 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              2067               6443 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             579.5              458.0 
[1] "1.0 - 2067.0 (579.5)" "2.0 - 6443.0 (458.0)"
[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        13        21         19
  14Q LOSS WILD-TYPE       4       98      105        36        49         49
                    vv
clus                 STAGE IIIB STAGE IV
  14Q LOSS MUTATED            2        6
  14Q LOSS WILD-TYPE          9       18
D66V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 18                 98
  STAGE IB                 27                105
  STAGE IIA                13                 36
  STAGE IIB                21                 49
  STAGE IIIA               19                 49
  STAGE IIIB                2                  9
  STAGE IV                  6                 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 LOSS MUTATED    25  65  12   4
  14Q LOSS WILD-TYPE 122 202  30  14
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               25                122
  T2               65                202
  T3               12                 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
  14Q LOSS MUTATED    58  30    18
  14Q LOSS WILD-TYPE 243  61    56
D66V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                  58                243
  N1                  30                 61
  N2+N3               18                 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
  14Q LOSS MUTATED    80   4   0   1  21
  14Q LOSS WILD-TYPE 246  14   1   3 102
D66V6, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                80                246
  M1                 4                 14
  M1A                0                  1
  M1B                1                  3
  MX                21                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"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    51  56
  14Q LOSS WILD-TYPE 204 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     51   56
  14Q LOSS WILD-TYPE  204  165
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               51                204
  MALE                 56                165
[1] 2 2
[1] FALSE
D66V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  14Q LOSS MUTATED                            3
  14Q LOSS WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  14Q LOSS MUTATED                                  22
  14Q LOSS WILD-TYPE                                72
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                   69
  14Q LOSS WILD-TYPE                                                234
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  14Q LOSS MUTATED                                            0
  14Q LOSS WILD-TYPE                                          5
                    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                                               1
  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)               69
  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                     1
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   14Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  72
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                234
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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     4 103
  14Q LOSS WILD-TYPE  17 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4  103
  14Q LOSS WILD-TYPE   17  352
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 4                 17
  YES              103                352
[1] 2 2
[1] FALSE
D66V11, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    77   0   0   5
  14Q LOSS WILD-TYPE 250  12   4  16
D66V12, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               77                250
  R1                0                 12
  R2                0                  4
  RX                5                 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
  14Q LOSS MUTATED                                  0     2
  14Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          14    75
  14Q LOSS WILD-TYPE                        21   292
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                      14                 21
  WHITE                                          75                292
[1] 4 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  83
  14Q LOSS WILD-TYPE   5 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   83
  14Q LOSS WILD-TYPE    5  262
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               83                262
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   159  36
  15Q LOSS WILD-TYPE 170  51
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               195                221 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                36                 51 
$`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-44-8120 TCGA-44-A47F 
         882          719          385           99          260          337 
TCGA-49-4501 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6761 TCGA-49-AARQ 
        1421          896         1700          890          354         6443 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5933 TCGA-50-5935 
        2174         2146          455          944         2370          653 
TCGA-50-5941 TCGA-50-5946 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 
         567          686         1015          255          105         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-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-7281 
         993         1239           25           67         1826           18 
TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
          35           95           40           34           54           19 
TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8205 
           3           31          100          600            4           33 
TCGA-55-8301 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8614 
          44            8           15          228            9          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 
          15           48           66           33           29           48 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8397 TCGA-62-A472 
        1952           28           47          162         1289          910 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
        1728         1686         1968         1959         1305          864 
TCGA-67-3770 TCGA-67-3772 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
          31          573          165          230          184           70 
TCGA-69-7979 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
          89          214          711          912          800          467 
TCGA-73-4675 TCGA-73-7499 TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 TCGA-78-7145 
          40          519         1970         1967         1965         1973 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7153 TCGA-78-7158 TCGA-78-7159 TCGA-78-7167 
        1988         1950          760         1963         1221         1937 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-80-5608 TCGA-86-7701 
        1972         1949         1952         1949         1972           11 
TCGA-86-7954 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 
        1963           13           24          479          482           19 
TCGA-86-8359 TCGA-86-8669 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 
          26           34           10           30          323         1940 
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-91-8499 TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 
          36           44          297          127          186           34 
TCGA-95-7562 TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
        1973          568           84          553          605          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-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV 
           6          111          102          827         1175         1946 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE 
        1967         1951         1954         1957         1944         1970 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1970         1955         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-A479 
        1938         1978          444         1970          535          486 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         466          287          351          415           76         1932 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-6742 
        1081          428          999          268          157          445 
TCGA-49-6743 TCGA-49-6745 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
         369          522          785         1499          246          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5942 TCGA-50-5944 TCGA-53-7624 TCGA-55-1594 
         267         1091          883          764         1986         1178 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6972 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
           2           24         1475         1233         2151         1170 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
         121            6            4          705           39           39 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8085 
          24           16          197           21            5           33 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
         462            6           26           47           15           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          66          674          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-73-A9RS 
        1600          131          164           38          621          305 
TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
        1956         1944         1093         1963         1202         1948 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1957         1961          678          215         1940         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-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 
        1971         1981         1954         1964         1965          824 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
        1959          630          422         1968          591          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
         745           10         1963          489          476           16 
TCGA-86-8281 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1955           35           45           18           15          455 
TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6849 TCGA-91-7771 
         405           14           39           60           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 
         505          174          218            2          377          477 
TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         476          830          121         1965         1932         1332 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 
          22          107         1965           87           15          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
         115          197          271           44          170          114 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 TCGA-MN-A4N5 TCGA-MP-A4T7 
         282          435          266          312           84         1954 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-S2-AA1A 
        1980         1951          142         1490          121 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                  1 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              6443               2696 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               553                455 
[1] "3.0 - 6443.0 (553.0)" "1.0 - 2696.0 (455.0)"
[1] "hr=" "1.4"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  15Q LOSS MUTATED         3       51       68        26        28         34
  15Q LOSS WILD-TYPE       2       65       64        23        42         34
                    vv
clus                 STAGE IIIB STAGE IV
  15Q LOSS MUTATED            6       10
  15Q LOSS WILD-TYPE          5       14
D67V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 51                 65
  STAGE IB                 68                 64
  STAGE IIA                26                 23
  STAGE IIB                28                 42
  STAGE IIIA               34                 34
  STAGE IIIB                6                  5
  STAGE IV                 10                 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
  15Q LOSS MUTATED    69 131  18   8
  15Q LOSS WILD-TYPE  78 136  24  10
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               69                 78
  T2              131                136
  T3               18                 24
  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   140  43    38
  15Q LOSS WILD-TYPE 161  48    36
D67V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                 140                161
  N1                  43                 48
  N2+N3               38                 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
  15Q LOSS MUTATED   156   7   0   2  60
  15Q LOSS WILD-TYPE 170  11   1   2  63
D67V6, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               156                170
  M1                 7                 11
  M1A                0                  1
  M1B                2                  2
  MX                60                 63
[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   124 102
  15Q LOSS WILD-TYPE 131 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    124  102
  15Q LOSS WILD-TYPE  131  119
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              124                131
  MALE                102                119
[1] 2 2
[1] FALSE
D67V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  15Q LOSS MUTATED                            6
  15Q LOSS WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  15Q LOSS MUTATED                                  33
  15Q LOSS WILD-TYPE                                61
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                  161
  15Q LOSS WILD-TYPE                                                142
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  15Q LOSS MUTATED                                            0
  15Q LOSS WILD-TYPE                                          5
                    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                                               2
  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                                        6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              161
  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                     2
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   15Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                142
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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    11 215
  15Q LOSS WILD-TYPE  10 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     11  215
  15Q LOSS WILD-TYPE   10  240
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                11                 10
  YES              215                240
[1] 2 2
[1] FALSE
D67V11, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED   154   6   2  11
  15Q LOSS WILD-TYPE 173   6   2  10
D67V12, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0              154                173
  R1                6                  6
  R2                2                  2
  RX               11                 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
  15Q LOSS MUTATED                                  1     4
  15Q LOSS WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                          17   174
  15Q LOSS WILD-TYPE                        18   193
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                      17                 18
  WHITE                                         174                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"
D67V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3 164
  15Q LOSS WILD-TYPE   4 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3  164
  15Q LOSS WILD-TYPE    4  181
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              164                181
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    72  18
  16P LOSS WILD-TYPE 257  69
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                90                326 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                18                 69 
$`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-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-49-4494 TCGA-49-4510 
         366          719          385           99         1081          896 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5066 TCGA-50-5068 
         445          369          522          354          944         1499 
TCGA-50-5946 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6971 
         686         1986          424          280           87           25 
TCGA-55-6986 TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 TCGA-55-7914 TCGA-55-8094 
        2151           40           34           19            3            4 
TCGA-55-8205 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8616 TCGA-55-A491 
          33           29           11            8           48         1952 
TCGA-62-8397 TCGA-62-8402 TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
        1289         1445         2067         2199         1246          910 
TCGA-64-1677 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-69-7763 TCGA-69-7974 
         628          864           31          610          690          184 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4662 TCGA-73-A9RS TCGA-75-6214 TCGA-78-7146 
         129          214          912          305         1970         1988 
TCGA-78-7149 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-83-5908 TCGA-86-6851 
        1093         1937         1972         1949          824         1959 
TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8073 TCGA-86-8672 TCGA-91-6829 
         422          591          745           13           15         1940 
TCGA-91-6831 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-95-7562 TCGA-95-7567 
         310          842          492           36         1973          568 
TCGA-95-8494 TCGA-95-A4VN TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-L4-A4E5 
          84          553          775          181          107          578 
TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TF TCGA-MP-A4TI 
           6          111          827         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-44-8120 
         218          557         1970          882          535          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-44-A4SU TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
          76         1932         1421          428          999          268 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 
         157         1700          890         6443         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          705           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          462          100            6 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 
         600           26           47           15           46           66 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8510 
         674          216           44           23           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-55-8620 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-62-8398 TCGA-62-8399 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
        1216         1970         2696         1728         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-67-3772 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-69-7764 TCGA-69-7765 TCGA-69-7973 
         422          202          186          414          165          230 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 
          70           89          382          100           77           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        1600          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-78-7150 TCGA-78-7152 
        1965         1973         1950         1944         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-78-7220 
         678          215         1940         1950         1934         1965 
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-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
          11          630         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          505          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-95-8039 TCGA-95-A4VK TCGA-95-A4VP 
         377          477          476          830          121          605 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8172 
         964         1965         1932         1332           22          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-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
         170          154          114          287          282          238 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 
         435          116          266          312          102         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
          84         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 TCGA-S2-AA1A 
        1490          121 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                  1 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              2199               6443 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             657.0              451.5 
[1] "3.0 - 2199.0 (657.0)" "1.0 - 6443.0 (451.5)"
[1] "hr=" "1.5"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  16P LOSS MUTATED         1       19       22        12        20         20
  16P LOSS WILD-TYPE       4       97      110        37        50         48
                    vv
clus                 STAGE IIIB STAGE IV
  16P LOSS MUTATED            6        7
  16P LOSS WILD-TYPE          5       17
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 19                 97
  STAGE IB                 22                110
  STAGE IIA                12                 37
  STAGE IIB                20                 50
  STAGE IIIA               20                 48
  STAGE IIIB                6                  5
  STAGE IV                  7                 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
  16P LOSS MUTATED    28  61  12   6
  16P LOSS WILD-TYPE 119 206  30  12
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               28                119
  T2               61                206
  T3               12                 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
  16P LOSS MUTATED    61  20    24
  16P LOSS WILD-TYPE 240  71    50
D68V5, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                  61                240
  N1                  20                 71
  N2+N3               24                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  16P LOSS MUTATED    73   5   1   1  27
  16P LOSS WILD-TYPE 253  13   0   3  96
D68V6, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                73                253
  M1                 5                 13
  M1A                1                  0
  M1B                1                  3
  MX                27                 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"
D68V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    52  55
  16P LOSS WILD-TYPE 203 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     52   55
  16P LOSS WILD-TYPE  203  166
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               52                203
  MALE                 55                166
[1] 2 2
[1] FALSE
D68V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16P LOSS MUTATED                            4
  16P LOSS WILD-TYPE                         11
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16P LOSS MUTATED                                  24
  16P LOSS WILD-TYPE                                70
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                   65
  16P LOSS WILD-TYPE                                                238
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16P LOSS MUTATED                                            0
  16P LOSS WILD-TYPE                                          5
                    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                                               2
  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)               65
  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                     2
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   16P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                238
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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     5 102
  16P LOSS WILD-TYPE  16 353
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5  102
  16P LOSS WILD-TYPE   16  353
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 5                 16
  YES              102                353
[1] 2 2
[1] FALSE
D68V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    71   1   1   3
  16P LOSS WILD-TYPE 256  11   3  18
D68V12, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               71                256
  R1                1                 11
  R2                1                  3
  RX                3                 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
  16P LOSS MUTATED                                  0     1
  16P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                          10    82
  16P LOSS WILD-TYPE                        25   285
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                      10                 25
  WHITE                                          82                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"
D68V14, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  76
  16P LOSS WILD-TYPE   4 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   76
  16P LOSS WILD-TYPE    4  269
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO               76                269
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    95  22
  16Q LOSS WILD-TYPE 234  65
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               117                299 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                 65 
$`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-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47B TCGA-49-4494 TCGA-49-4510 
         719          385           99          287         1081          896 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5066 
         445          369          522          354         2146          944 
TCGA-50-5068 TCGA-50-5946 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 
        1499          686         1986          424          280         1479 
TCGA-55-5899 TCGA-55-6971 TCGA-55-6986 TCGA-55-7281 TCGA-55-7576 TCGA-55-7727 
          87           25         2151           18           40           34 
TCGA-55-7903 TCGA-55-8205 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8616 
          19           33           29           11            8           48 
TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 TCGA-62-8397 TCGA-62-A46U 
          66           29         1952           28         1289         2067 
TCGA-62-A472 TCGA-64-1677 TCGA-64-5774 TCGA-64-5778 TCGA-67-3770 TCGA-67-3771 
         910          628         1959         1305           31          610 
TCGA-69-7763 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K 
         690          184           70           89          129          214 
TCGA-73-4658 TCGA-73-4662 TCGA-73-A9RS TCGA-75-6214 TCGA-78-7146 TCGA-78-7149 
        1600          912          305         1970         1988         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7159 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
        1963         1202         1221         1937         1972         1949 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 
         824         1959          630          422          591          745 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8359 TCGA-86-8672 TCGA-91-6829 TCGA-91-6831 
          13          479           26           15         1940          310 
TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-93-7348 TCGA-95-7562 TCGA-95-7567 
         842          492           36          127         1973          568 
TCGA-95-8494 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
          84          553          964          775          181          107 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N1 
         238          578          116            6          111          827 
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-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         260          486          466          337          351          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
          76         1932         1421          428          999          268 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-AARQ TCGA-50-5045 TCGA-50-5051 
         157         1700          890         6443         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          705           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          462          100            6          600           26 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
           4           47           15           46           66          674 
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-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 
         106           33           42           48            1            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-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
        2199         1246         1728         1189         1686         1126 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
        1968           62          864         1559          866          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-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 
         186          414          165          230          382          100 
TCGA-69-8254 TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
          77           61          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-78-7147 TCGA-78-7148 TCGA-78-7153 
        1956         1965         1973         1950         1944          760 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 
        1948         1957         1961         1963          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 
        1940         1950         1934         1965         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-86-7701 TCGA-86-7714 
        1954         1964         1965         1972           11         1968 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 
        1963          508           10         1963           24          489 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8585 
         476          482           16         1955           19           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
          45           34           18          455          405           10 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 
          30           14           39          323           60           79 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
         417          372          224           35          505          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
          44          218          297          186           34            2 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VP 
         377          477          476          830          121          605 
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-97-8547 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-L4-A4E6 TCGA-L9-A50W 
         154          114          287          282          435          266 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         312          102         1175           84         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 TCGA-S2-AA1A 
        1970          142         1971         1490          121 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                  1 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              2151               6443 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               630                435 
[1] "6.0 - 2151.0 (630.0)" "1.0 - 6443.0 (435.0)"
[1] "hr=" "1.3"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  16Q LOSS MUTATED         1       30       34        13        23         20
  16Q LOSS WILD-TYPE       4       86       98        36        47         48
                    vv
clus                 STAGE IIIB STAGE IV
  16Q LOSS MUTATED            6        7
  16Q LOSS WILD-TYPE          5       17
D69V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 30                 86
  STAGE IB                 34                 98
  STAGE IIA                13                 36
  STAGE IIB                23                 47
  STAGE IIIA               20                 48
  STAGE IIIB                6                  5
  STAGE IV                  7                 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
  16Q LOSS MUTATED    42  75  12   5
  16Q LOSS WILD-TYPE 105 192  30  13
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               42                105
  T2               75                192
  T3               12                 30
  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    80  26    25
  16Q LOSS WILD-TYPE 221  65    49
D69V5, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                  80                221
  N1                  26                 65
  N2+N3               25                 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
  16Q LOSS MUTATED    94   5   1   1  32
  16Q LOSS WILD-TYPE 232  13   0   3  91
D69V6, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                94                232
  M1                 5                 13
  M1A                1                  0
  M1B                1                  3
  MX                32                 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"
D69V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    67  67
  16Q LOSS WILD-TYPE 188 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     67   67
  16Q LOSS WILD-TYPE  188  154
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               67                188
  MALE                 67                154
[1] 2 2
[1] FALSE
D69V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  16Q LOSS MUTATED                            5
  16Q LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  16Q LOSS MUTATED                                  29
  16Q LOSS WILD-TYPE                                65
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                   84
  16Q LOSS WILD-TYPE                                                219
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  16Q LOSS MUTATED                                            0
  16Q LOSS WILD-TYPE                                          5
                    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                                               2
  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)               84
  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                     2
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   16Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                219
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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     5 129
  16Q LOSS WILD-TYPE  16 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5  129
  16Q LOSS WILD-TYPE   16  326
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 5                 16
  YES              129                326
[1] 2 2
[1] FALSE
D69V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    92   1   1   3
  16Q LOSS WILD-TYPE 235  11   3  18
D69V12, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               92                235
  R1                1                 11
  R2                1                  3
  RX                3                 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
  16Q LOSS MUTATED                                  0     2
  16Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                          11   103
  16Q LOSS WILD-TYPE                        24   264
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                      11                 24
  WHITE                                         103                264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     4  95
  16Q LOSS WILD-TYPE   3 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4   95
  16Q LOSS WILD-TYPE    3  250
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO               95                250
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   142  32
  17P LOSS WILD-TYPE 187  55
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               174                242 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                32                 55 
$`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-44-7667 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 
         366          218          557          882          385           99 
TCGA-44-8120 TCGA-44-A47B TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
         260          287          428          268          896          157 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARQ TCGA-50-5051 
         369          890          522          354         6443          455 
TCGA-50-5068 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 
        1499          267          567          764         1015          255 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
        1986         1971          424          701         1178         1375 
TCGA-55-6712 TCGA-55-6972 TCGA-55-6985 TCGA-55-7281 TCGA-55-7573 TCGA-55-7576 
          24         1475         1233           18            4           40 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          39           34           19          197           21            3 
TCGA-55-7994 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8097 TCGA-55-8205 
          31          100          600           26           15           33 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-A48X TCGA-55-A48Y 
         228            9          202          536           33           42 
TCGA-55-A48Z TCGA-55-A491 TCGA-62-8397 TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 
          29         1952         1289         2067          910         1728 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        1686         1968         1959          866           31          610 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
         427          174          422          202          186          414 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-8255 TCGA-69-A59K TCGA-73-4658 
         165          184           70          129          214         1600 
TCGA-73-4659 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7031 
         711          519          305         1970         1967         1965 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7150 TCGA-78-7159 TCGA-78-7535 TCGA-78-7536 
        1973         1988         1963         1221         1972         1949 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-80-5608 
         327          881         1952         1949         1981         1972 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 
          11          630          591         1963          745         1963 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
          13          479          476          482           16           19 
TCGA-86-8668 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-93-7347 
          45          310          372          842          492          297 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
          34         1973          568          377          477          476 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7554 
         830           84          121          553          605          775 
TCGA-97-7937 TCGA-97-8175 TCGA-97-8547 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 
         181           87          148          392          427          170 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A8F4 
         154          287          282          578          266          102 
TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 
        1175         1954         1957         1970         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-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F 
        1970          535          719          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-49-4506 TCGA-49-4514 TCGA-49-6742 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
         999         1700          445         2174         2146          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-50-5942 TCGA-50-5946 TCGA-50-8460 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 
         883          686          105          280         1479           87 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 
           2          993         1239           25           67         1826 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 
        2151         1170           35          121            6           95 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7995 
         705           39           24           54           16            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 
          33          462            6            4           47           46 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          66          674          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          505          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-L9-A743 
         114          238          435          116            6          312 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         111          827           84         1946         1967         1951 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI 
        1954         1980         1951         1944          142         1955 
TCGA-MP-A4TK TCGA-S2-AA1A 
        1971          121 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                  1 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              6443               2696 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             505.5              455.0 
[1] "3.0 - 6443.0 (505.5)" "1.0 - 2696.0 (455.0)"
[1] "hr=" "1.4"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  17P LOSS MUTATED         3       37       57        24        35         34
  17P LOSS WILD-TYPE       2       79       75        25        35         34
                    vv
clus                 STAGE IIIB STAGE IV
  17P LOSS MUTATED            4       10
  17P LOSS WILD-TYPE          7       14
D70V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 37                 79
  STAGE IB                 57                 75
  STAGE IIA                24                 25
  STAGE IIB                35                 35
  STAGE IIIA               34                 34
  STAGE IIIB                4                  7
  STAGE IV                 10                 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
  17P LOSS MUTATED    54 124  18   7
  17P LOSS WILD-TYPE  93 143  24  11
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               54                 93
  T2              124                143
  T3               18                 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   125  42    33
  17P LOSS WILD-TYPE 176  49    41
D70V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                 125                176
  N1                  42                 49
  N2+N3               33                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  17P LOSS MUTATED   141   9   0   0  53
  17P LOSS WILD-TYPE 185   9   1   4  70
D70V6, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               141                185
  M1                 9                  9
  M1A                0                  1
  M1B                0                  4
  MX                53                 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"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   117  87
  17P LOSS WILD-TYPE 138 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    117   87
  17P LOSS WILD-TYPE  138  134
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              117                138
  MALE                 87                134
[1] 2 2
[1] FALSE
D70V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17P LOSS MUTATED                            6
  17P LOSS WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17P LOSS MUTATED                                  38
  17P LOSS WILD-TYPE                                56
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                  140
  17P LOSS WILD-TYPE                                                163
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17P LOSS MUTATED                                            2
  17P LOSS WILD-TYPE                                          3
                    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                                               3
  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                                        6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              140
  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                     3
  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)                163
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          3
  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     4 200
  17P LOSS WILD-TYPE  17 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  200
  17P LOSS WILD-TYPE   17  255
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 4                 17
  YES              200                255
[1] 2 2
[1] FALSE
D70V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   142   4   1  10
  17P LOSS WILD-TYPE 185   8   3  11
D70V12, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              142                185
  R1                4                  8
  R2                1                  3
  RX               10                 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                          17   156
  17P LOSS WILD-TYPE                        18   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                      17                 18
  WHITE                                         156                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     5 144
  17P LOSS WILD-TYPE   2 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5  144
  17P LOSS WILD-TYPE    2  201
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  2
  NOT HISPANIC OR LATINO              144                201
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    38  12
  17Q LOSS WILD-TYPE 291  75
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                50                366 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                 75 
$`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-49-6744 TCGA-49-6761 TCGA-49-AARQ TCGA-50-5051 TCGA-50-5068 TCGA-53-7624 
         890          354         6443          455         1499         1986 
TCGA-55-1596 TCGA-55-6712 TCGA-55-7576 TCGA-55-8091 TCGA-55-8092 TCGA-55-8511 
        1375           24           40          600           26            9 
TCGA-55-8614 TCGA-62-8397 TCGA-64-1676 TCGA-67-6217 TCGA-69-7764 TCGA-69-A59K 
         536         1289         1728          422          414          214 
TCGA-73-A9RS TCGA-75-7025 TCGA-75-7031 TCGA-78-7146 TCGA-78-7535 TCGA-78-7536 
         305         1967         1965         1988         1972         1949 
TCGA-78-8655 TCGA-86-7701 TCGA-86-8280 TCGA-91-6840 TCGA-91-7771 TCGA-95-7562 
        1981           11           16          372          492         1973 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 
         476          121          605          154          287          578 
TCGA-L9-A8F4 TCGA-MP-A5C7 
         102         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-49-6745 TCGA-50-5045 
         896         1700          445          369          522         2174 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
        2146          785          944          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-53-7626 TCGA-53-7813 
         686         1015          255          105         1971          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-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 
         993         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-55-7724 TCGA-55-7725 TCGA-55-7726 
           6            4           95          705           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          462 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
         100            6            4           47           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
          46           66          674          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          505          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-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7546 
         377          477          830           84          553          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-97-8552 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-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
         459           44          170          114          282          238 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
         435          116            6          266          312          111 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 
         827         1175           84         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-S2-AA1A 
        1970         1970          142         1955         1971          121 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                  1 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              6443               2696 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             484.0              471.5 
[1] "9.0 - 6443.0 (484.0)" "1.0 - 2696.0 (471.5)"
[1] "hr=" "1.3"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  17Q LOSS MUTATED         2        7       15         7        11         11
  17Q LOSS WILD-TYPE       3      109      117        42        59         57
                    vv
clus                 STAGE IIIB STAGE IV
  17Q LOSS MUTATED            2        2
  17Q LOSS WILD-TYPE          9       22
D71V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                  7                109
  STAGE IB                 15                117
  STAGE IIA                 7                 42
  STAGE IIB                11                 59
  STAGE IIIA               11                 57
  STAGE IIIB                2                  9
  STAGE IV                  2                 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
  17Q LOSS MUTATED     9  39   7   2
  17Q LOSS WILD-TYPE 138 228  35  16
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                9                138
  T2               39                228
  T3                7                 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
  17Q LOSS MUTATED    32  13    11
  17Q LOSS WILD-TYPE 269  78    63
D71V5, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                  32                269
  N1                  13                 78
  N2+N3               11                 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
  17Q LOSS MUTATED    38   2   0   0  16
  17Q LOSS WILD-TYPE 288  16   1   4 107
D71V6, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                38                288
  M1                 2                 16
  M1A                0                  1
  M1B                0                  4
  MX                16                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"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    32  25
  17Q LOSS WILD-TYPE 223 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     32   25
  17Q LOSS WILD-TYPE  223  196
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               32                223
  MALE                 25                196
[1] 2 2
[1] FALSE
D71V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  17Q LOSS MUTATED                            1
  17Q LOSS WILD-TYPE                         14
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  17Q LOSS MUTATED                                  11
  17Q LOSS WILD-TYPE                                83
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                   42
  17Q LOSS WILD-TYPE                                                261
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  17Q LOSS MUTATED                                            0
  17Q LOSS WILD-TYPE                                          5
                    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                                             5
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  17Q LOSS MUTATED                              1
  17Q LOSS WILD-TYPE                            6
D71V9, multiclass
                                                    clus
vv                                                   17Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               42
  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                                         14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                261
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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                       5
  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  55
  17Q LOSS WILD-TYPE  19 400
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   55
  17Q LOSS WILD-TYPE   19  400
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 2                 19
  YES               55                400
[1] 2 2
[1] FALSE
D71V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    41   2   0   3
  17Q LOSS WILD-TYPE 286  10   4  18
D71V12, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               41                286
  R1                2                 10
  R2                0                  4
  RX                3                 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
  17Q LOSS MUTATED                                  0     1
  17Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           6    43
  17Q LOSS WILD-TYPE                        29   324
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                       6                 29
  WHITE                                          43                324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  43
  17Q LOSS WILD-TYPE   6 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   43
  17Q LOSS WILD-TYPE    6  302
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               43                302
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   112  29
  18P LOSS WILD-TYPE 217  58
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               141                275 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                29                 58 
$`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          462            6          600           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-73-A9RS TCGA-75-6214 TCGA-75-7025 
         800          131          519          305         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7150 TCGA-78-7161 TCGA-78-7167 
        1956         1965         1988         1963          215         1937 
TCGA-78-7535 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 
        1972         1954          824         1959           11         1968 
TCGA-86-7954 TCGA-86-8073 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
        1963           13          476          482           16           19 
TCGA-86-8672 TCGA-91-6830 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 
          15           60          417          842          224          492 
TCGA-91-A4BD TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-95-8039 
         218          127           34          568          476          830 
TCGA-95-8494 TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 
          84          553         1965         1932          181           22 
TCGA-97-8174 TCGA-97-8547 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1965          148          154          114          287          282 
TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SW TCGA-MP-A4T2 
         578          266          111          102         1967         1951 
TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TI 
        1954         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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         354         6443         2174         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
         944         1499          282          267         1091          653 
TCGA-50-5942 TCGA-50-5944 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ 
         883          764          255          105          424          280 
TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
         701         1479           87            2          993           24 
TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 
        1239           67         1826         2151         1170          121 
TCGA-55-7570 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
           6          705           39           34           54           19 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
          16           21            3           31            5           33 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 
         100           26            4           47           33           46 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
         674          216           44           23           29           11 
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-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
         536           15           49          106           33           42 
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-64-1676 TCGA-64-1677 TCGA-64-1678 
        1445         2067         2199         1728          628         1189 
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-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         427          385          174          202          186          690 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
         414          230          184           70          382          100 
TCGA-69-8254 TCGA-69-8255 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 
          77          129         1600          711          912          467 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-78-7145 TCGA-78-7147 
          40          164           38          621         1973         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1944         1093         1202          760         1948         1957 
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-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        1934         1965         1949         1944          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-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 
        1965         1972          630          422          591          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
         745           10         1963           24          479          489 
TCGA-86-8281 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
        1955           26           35           45           34           18 
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-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6849 
         323         1940          310           79          372           35 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7347 TCGA-93-8067 
         505          174           36           44          297          186 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VP 
           2         1973          377          477          121          605 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
         964         1332          775          107          182           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
         147           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-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         116            6          312          827         1175           84 
TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
        1946         1954         1957         1980         1951         1944 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970          142         1971         1490          121 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  2 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              2370               6443 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               519                455 
[1] "1.0 - 2370.0 (519.0)" "2.0 - 6443.0 (455.0)"
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  18P LOSS MUTATED         1       26       48        20        31         19
  18P LOSS WILD-TYPE       4       90       84        29        39         49
                    vv
clus                 STAGE IIIB STAGE IV
  18P LOSS MUTATED            5       13
  18P LOSS WILD-TYPE          6       11
D72V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 26                 90
  STAGE IB                 48                 84
  STAGE IIA                20                 29
  STAGE IIB                31                 39
  STAGE IIIA               19                 49
  STAGE IIIB                5                  6
  STAGE IV                 13                 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
  18P LOSS MUTATED    42 100  15   6
  18P LOSS WILD-TYPE 105 167  27  12
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               42                105
  T2              100                167
  T3               15                 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
  18P LOSS MUTATED    99  39    23
  18P LOSS WILD-TYPE 202  52    51
D72V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                  99                202
  N1                  39                 52
  N2+N3               23                 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
  18P LOSS MUTATED   100  11   0   1  51
  18P LOSS WILD-TYPE 226   7   1   3  72
D72V6, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               100                226
  M1                11                  7
  M1A                0                  1
  M1B                1                  3
  MX                51                 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"
D72V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   100  63
  18P LOSS WILD-TYPE 155 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    100   63
  18P LOSS WILD-TYPE  155  158
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              100                155
  MALE                 63                158
[1] 2 2
[1] FALSE
D72V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18P LOSS MUTATED                            5
  18P LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18P LOSS MUTATED                                  32
  18P LOSS WILD-TYPE                                62
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                  106
  18P LOSS WILD-TYPE                                                197
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18P LOSS MUTATED                                            1
  18P LOSS WILD-TYPE                                          4
                    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                                               1
  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                                        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              106
  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                     1
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   18P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                197
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  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     5 158
  18P LOSS WILD-TYPE  16 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5  158
  18P LOSS WILD-TYPE   16  297
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 5                 16
  YES              158                297
[1] 2 2
[1] FALSE
D72V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED   110   5   3   5
  18P LOSS WILD-TYPE 217   7   1  16
D72V12, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0              110                217
  R1                5                  7
  R2                3                  1
  RX                5                 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
  18P LOSS MUTATED                                  0     2
  18P LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          14   119
  18P LOSS WILD-TYPE                        21   248
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                      14                 21
  WHITE                                         119                248
[1] 4 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     2 116
  18P LOSS WILD-TYPE   5 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2  116
  18P LOSS WILD-TYPE    5  229
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              116                229
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   129  39
  18Q LOSS WILD-TYPE 200  48
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               168                248 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                39                 48 
$`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-49-6761 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5933 
         369          354          944         1499          246         2370 
TCGA-50-5941 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 
         567          686         1015         1986         1971         1178 
TCGA-55-1596 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6985 
        1375           24           25         1475           67         1233 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 
          18           35            4           95           40           39 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7910 TCGA-55-7994 TCGA-55-8087 TCGA-55-8090 
          39           24          197           31          462            6 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8207 TCGA-55-8507 TCGA-55-8616 
         600            4           15           66            8           48 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-62-8397 
          29           48         1952            1           28         1289 
TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 
        2067         1246          910         1686         1968           62 
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-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 TCGA-69-7979 TCGA-69-8254 
         141          422          202          165           89           77 
TCGA-69-A59K TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-7499 TCGA-73-A9RS 
         214          912          800          131          519          305 
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-78-7150 TCGA-78-7155 TCGA-78-7161 TCGA-78-7535 TCGA-78-7536 
        1950         1963         1957          215         1972         1949 
TCGA-78-7539 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
         327         1954          824         1959           11          630 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8074 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        1968         1963           24          476          482           16 
TCGA-86-8672 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
          15         1940           60          417          842          224 
TCGA-91-7771 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-95-7567 TCGA-95-7947 
         492           44          218          127          568          477 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 
         830           84          553         1965         1932          181 
TCGA-97-7941 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-J2-8192 TCGA-J2-8194 
          22         1965          147          148          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N4 
         287          282          578          266          102         1175 
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-AARQ 
         268          896         1700          890          522         6443 
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          705           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-55-8208 TCGA-55-8299 TCGA-55-8301 
          47           33           46          674          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          23           29           11           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-A494 TCGA-55-A4DF 
          66          106           33           42            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-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 
        1728          628         1189         1126         1959          864 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
         427          385          174          186          690          414 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 
         230          184           70          382          100          129 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
          61         1600          711          467           40          164 
TCGA-73-4677 TCGA-73-7498 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
          38          621         1944         1093         1202          760 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 
        1948         1961         1963         1221          678         1940 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7540 
        1950         1934         1937         1965         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-80-5608 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
        1965         1972          422          591          508          745 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8281 
          10         1963           13          479          489         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-86-8673 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-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6849 TCGA-91-8496 
         323          310           79          372           35          505 
TCGA-91-8497 TCGA-91-8499 TCGA-93-7347 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         174           36          297          186           34            2 
TCGA-95-7562 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 
        1973          377          476          121          605          964 
TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 
        1332          775          107          182           87           15 
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-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
          44          170          238          435          116            6 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 
         312          111          827           84         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 TCGA-S2-AA1A 
        1490          121 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                  2 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              2370               6443 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             505.5              456.0 
[1] "1.0 - 2370.0 (505.5)" "2.0 - 6443.0 (456.0)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  18Q LOSS MUTATED         1       32       55        25        39         26
  18Q LOSS WILD-TYPE       4       84       77        24        31         42
                    vv
clus                 STAGE IIIB STAGE IV
  18Q LOSS MUTATED            5       13
  18Q LOSS WILD-TYPE          6       11
D73V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 32                 84
  STAGE IB                 55                 77
  STAGE IIA                25                 24
  STAGE IIB                39                 31
  STAGE IIIA               26                 42
  STAGE IIIB                5                  6
  STAGE IV                 13                 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
  18Q LOSS MUTATED    51 119  19   8
  18Q LOSS WILD-TYPE  96 148  23  10
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               51                 96
  T2              119                148
  T3               19                 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
  18Q LOSS MUTATED   116  48    29
  18Q LOSS WILD-TYPE 185  43    45
D73V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                 116                185
  N1                  48                 43
  N2+N3               29                 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
  18Q LOSS MUTATED   126  11   0   1  57
  18Q LOSS WILD-TYPE 200   7   1   3  66
D73V6, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               126                200
  M1                11                  7
  M1A                0                  1
  M1B                1                  3
  MX                57                 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   116  81
  18Q LOSS WILD-TYPE 139 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    116   81
  18Q LOSS WILD-TYPE  139  140
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              116                139
  MALE                 81                140
[1] 2 2
[1] FALSE
D73V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  18Q LOSS MUTATED                            6
  18Q LOSS WILD-TYPE                          9
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  18Q LOSS MUTATED                                  41
  18Q LOSS WILD-TYPE                                53
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                  128
  18Q LOSS WILD-TYPE                                                175
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  18Q LOSS MUTATED                                            1
  18Q LOSS WILD-TYPE                                          4
                    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                                               1
  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                                        6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                41
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              128
  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                     1
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   18Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                175
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  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     6 191
  18Q LOSS WILD-TYPE  15 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      6  191
  18Q LOSS WILD-TYPE   15  264
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 6                 15
  YES              191                264
[1] 2 2
[1] FALSE
D73V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   134   8   3   4
  18Q LOSS WILD-TYPE 193   4   1  17
D73V12, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              134                193
  R1                8                  4
  R2                3                  1
  RX                4                 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
  18Q LOSS MUTATED                                  0     1
  18Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          14   148
  18Q LOSS WILD-TYPE                        21   219
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                      14                 21
  WHITE                                         148                219
[1] 4 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     4 135
  18Q LOSS WILD-TYPE   3 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4  135
  18Q LOSS WILD-TYPE    3  210
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  3
  NOT HISPANIC OR LATINO              135                210
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED   149  47
  19P LOSS WILD-TYPE 180  40
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               196                220 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                47                 40 
$`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-95-A4VN TCGA-97-8171 
           2          568          476          121          553          107 
TCGA-97-8174 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD 
        1965          392          427          170          154          287 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         578          116          111          102           84         1946 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF 
        1954         1954         1957         1951         1944         1970 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
         142         1955         1971         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-49-AARQ TCGA-50-5045 TCGA-50-5049 
         157         1700          354         6443         2174         2146 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5933 TCGA-50-5935 
         785          944         1499          282         2370          653 
TCGA-50-5942 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1595 TCGA-55-6543 
         883          105         1986         1971         1479            2 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
         993           24         1239           67         1826         1233 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
        2151         1170           18           35          121            4 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
          95          705           39           39           24           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
          19           16           21          462            6          600 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
          47           15           33           46           66          674 
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-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
         146          202           15           49           66          106 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-62-8399 TCGA-62-A46V 
          42           29           48            1         2696         2199 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 
         910          628         1189         1686         1126           62 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
        1559          866          610          427          174          141 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
         422          202          165          230          184           89 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4658 TCGA-73-4662 TCGA-73-4675 TCGA-73-4676 
         100           77         1600          912           40          164 
TCGA-73-A9RS TCGA-78-7145 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
         305         1973         1202         1948         1957         1963 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7220 TCGA-78-7537 TCGA-78-7540 
         678          215         1950         1965         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-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-8054 
        1965          824         1959          630         1968          745 
TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
        1963          489          476           19           26           35 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 
          45           18          455          405           14           39 
TCGA-91-6835 TCGA-91-6847 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
          79          842          505          174           36          218 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
         297          127          186         1973          377          477 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         830           84          605          964         1965         1932 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8172 TCGA-97-8175 
        1332          775          181           22          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-99-8028 TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
         459           44          114          282          238          435 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SW 
           6          266          312          827         1175         1967 
TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-S2-AA1A 
        1951         1980         1970          121 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                  1 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              2067               6443 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             520.5              449.5 
[1] "2.0 - 2067.0 (520.5)" "1.0 - 6443.0 (449.5)"
[1] "hr=" "1.5"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  19P LOSS MUTATED         3       45       57        26        37         35
  19P LOSS WILD-TYPE       2       71       75        23        33         33
                    vv
clus                 STAGE IIIB STAGE IV
  19P LOSS MUTATED            7       15
  19P LOSS WILD-TYPE          4        9
D74V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 45                 71
  STAGE IB                 57                 75
  STAGE IIA                26                 23
  STAGE IIB                37                 33
  STAGE IIIA               35                 33
  STAGE IIIB                7                  4
  STAGE IV                 15                  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
  19P LOSS MUTATED    62 134  17  10
  19P LOSS WILD-TYPE  85 133  25   8
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               62                 85
  T2              134                133
  T3               17                 25
  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   134  50    37
  19P LOSS WILD-TYPE 167  41    37
D74V5, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                 134                167
  N1                  50                 41
  N2+N3               37                 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
  19P LOSS MUTATED   162  12   1   2  46
  19P LOSS WILD-TYPE 164   6   0   2  77
D74V6, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               162                164
  M1                12                  6
  M1A                1                  0
  M1B                2                  2
  MX                46                 77
[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   107 118
  19P LOSS WILD-TYPE 148 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    107  118
  19P LOSS WILD-TYPE  148  103
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE              107                148
  MALE                118                103
[1] 2 2
[1] FALSE
D74V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19P LOSS MUTATED                            5
  19P LOSS WILD-TYPE                         10
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19P LOSS MUTATED                                  49
  19P LOSS WILD-TYPE                                45
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                  144
  19P LOSS WILD-TYPE                                                159
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19P LOSS MUTATED                                            0
  19P LOSS WILD-TYPE                                          5
                    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                                               2
  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)              144
  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                     2
  MUCINOUS (COLLOID) CARCINOMA                                      3
                                                    clus
vv                                                   19P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                159
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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     7 218
  19P LOSS WILD-TYPE  14 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      7  218
  19P LOSS WILD-TYPE   14  237
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 7                 14
  YES              218                237
[1] 2 2
[1] FALSE
D74V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED   156   2   3  10
  19P LOSS WILD-TYPE 171  10   1  11
D74V12, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0              156                171
  R1                2                 10
  R2                3                  1
  RX               10                 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
  19P LOSS MUTATED                                  1     4
  19P LOSS WILD-TYPE                                0     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                          15   170
  19P LOSS WILD-TYPE                        20   197
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                      15                 20
  WHITE                                         170                197
[1] 4 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     3 158
  19P LOSS WILD-TYPE   4 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3  158
  19P LOSS WILD-TYPE    4  187
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              158                187
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    91  30
  19Q LOSS WILD-TYPE 238  57
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               121                295 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                30                 57 
$`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-86-8279 
          11          591         1963          508           24          482 
TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 
          34           15           10           30          323         1940 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
         310          417          372          224           35          492 
TCGA-91-A4BC TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VN 
          44           34          568          476           84          553 
TCGA-97-8171 TCGA-99-7458 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 
         107          392          170          154          287          578 
TCGA-L9-A7SV TCGA-MP-A4SV TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TI TCGA-MP-A4TK 
         111         1946         1957         1951         1955         1971 
TCGA-MP-A5C7 
        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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         354         6443         2174         2146          785          944 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5942 
        1499          282          267         2370          653          883 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 
         255          105         1986         1971          280         1479 
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-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
         121            4           95           40          705           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-55-7914 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
          21            3          462          100            6          600 
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-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          66          674          216           44           23           29 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
          11           15          228            3          146          202 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y 
         536           15           49           66          106           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-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 
        1970         2696         2067         2199          910          628 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
        1189         1686         1126         1959           62         1305 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 
         864         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-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 
         414          165          230          184           89          382 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 
         100           77         1600          912          467           40 
TCGA-73-4676 TCGA-73-A9RS TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 
         164          305         1967         1973         1950         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-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 
         678          215         1950         1934         1965         1944 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
         327          881          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-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
         630          422         1968          745           10         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-86-8671 TCGA-86-8673 
          19           26           35           45           18          455 
TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 
         405           14           39           60           79          842 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
         505          174           36          218          297          127 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 
         186            2         1973          377          477          830 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         121          605          964         1965         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
         775          181           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-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
         427          459           44          114          282          238 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 
         435          116            6          266          312          102 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
         827         1175           84         1967         1951         1954 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
        1954         1980         1944         1970         1970          142 
TCGA-S2-AA1A 
         121 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                  1 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1997               6443 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               567                427 
[1] "5.0 - 1997.0 (567.0)" "1.0 - 6443.0 (427.0)"
[1] "hr=" "1.4"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  19Q LOSS MUTATED         1       28       35        14        26         23
  19Q LOSS WILD-TYPE       4       88       97        35        44         45
                    vv
clus                 STAGE IIIB STAGE IV
  19Q LOSS MUTATED            7       11
  19Q LOSS WILD-TYPE          4       13
D75V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   1                  4
  STAGE IA                 28                 88
  STAGE IB                 35                 97
  STAGE IIA                14                 35
  STAGE IIB                26                 44
  STAGE IIIA               23                 45
  STAGE IIIB                7                  4
  STAGE IV                 11                 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
  19Q LOSS MUTATED    36  86  13   9
  19Q LOSS WILD-TYPE 111 181  29   9
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               36                111
  T2               86                181
  T3               13                 29
  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  33    25
  19Q LOSS WILD-TYPE 216  58    49
D75V5, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                  85                216
  N1                  33                 58
  N2+N3               25                 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
  19Q LOSS MUTATED   105  10   1   0  27
  19Q LOSS WILD-TYPE 221   8   0   4  96
D75V6, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               105                221
  M1                10                  8
  M1A                1                  0
  M1B                0                  4
  MX                27                 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"
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    71  74
  19Q LOSS WILD-TYPE 184 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     71   74
  19Q LOSS WILD-TYPE  184  147
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               71                184
  MALE                 74                147
[1] 2 2
[1] FALSE
D75V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  19Q LOSS MUTATED                            2
  19Q LOSS WILD-TYPE                         13
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  19Q LOSS MUTATED                                  32
  19Q LOSS WILD-TYPE                                62
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                   94
  19Q LOSS WILD-TYPE                                                209
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  19Q LOSS MUTATED                                            0
  19Q LOSS WILD-TYPE                                          5
                    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                                               3
  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)               94
  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                     3
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   19Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                209
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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     4 141
  19Q LOSS WILD-TYPE  17 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4  141
  19Q LOSS WILD-TYPE   17  314
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 4                 17
  YES              141                314
[1] 2 2
[1] FALSE
D75V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    97   2   3   5
  19Q LOSS WILD-TYPE 230  10   1  16
D75V12, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               97                230
  R1                2                 10
  R2                3                  1
  RX                5                 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 LOSS MUTATED                                  0     4
  19Q LOSS WILD-TYPE                                1     2
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           8   109
  19Q LOSS WILD-TYPE                        27   258
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                       8                 27
  WHITE                                         109                258
[1] 4 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     2 102
  19Q LOSS WILD-TYPE   5 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2  102
  19Q LOSS WILD-TYPE    5  243
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              102                243
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    68  24
  20P LOSS WILD-TYPE 261  63
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                92                324 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                 63 
$`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-44-3918 TCGA-44-3919 TCGA-44-6779 
        1280         1301          246         1036          190         1978 
TCGA-44-A47A TCGA-44-A47G TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-49-6743 
         466          351         1421          428          157          369 
TCGA-49-6745 TCGA-49-AARQ TCGA-50-5051 TCGA-50-5072 TCGA-50-5933 TCGA-50-5944 
         522         6443          455          246         2370          764 
TCGA-50-6597 TCGA-53-7624 TCGA-55-1594 TCGA-55-1595 TCGA-55-6712 TCGA-55-6980 
        1015         1986         1178         1479           24           67 
TCGA-55-7283 TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 TCGA-55-7994 
          35           39           34           19           16           31 
TCGA-55-8090 TCGA-55-8092 TCGA-55-8207 TCGA-55-8506 TCGA-55-8616 TCGA-62-8397 
           6           26           66           11           48         1289 
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-64-1681 TCGA-64-5781 TCGA-67-3770 TCGA-67-3773 TCGA-67-6216 TCGA-69-7761 
        1968         1559           31          427          141          186 
TCGA-69-7974 TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 
         184          214          800          131           40          519 
TCGA-75-6214 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7158 TCGA-78-7535 
        1970         1973         1988         1944         1963         1972 
TCGA-78-7537 TCGA-78-8660 TCGA-86-6851 TCGA-86-7953 TCGA-86-7955 TCGA-86-8280 
        1944         1954         1959          591          508           16 
TCGA-86-8673 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6848 TCGA-93-7347 
         455          323          310           79          224          297 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-97-8177 TCGA-99-7458 TCGA-99-8033 
          34            2         1973          147          392          170 
TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T8 
         578            6         1175         1946         1967         1957 
TCGA-MP-A4TC TCGA-MP-A4TI 
        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-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        1130         1163          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-44-7659 TCGA-44-7660 
         705         1938         1942         1864          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-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 
         337          415           76         1932         1081          999 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6761 
         268          896         1700          445          890          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
        2174         2146          785          944         1499          282 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
         267         1091          653          567          883          686 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         255          105         1971          424          280          701 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 
        1375           87            2          993         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-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
         121            6            4           95           40          705 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          39           24           54          197           21            3 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 
           5           33          462          100          600            4 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
          47           15           33           46          674          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
          44           23           29            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-55-8619 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-A494 TCGA-55-A4DF 
          48         1952            1           28            5           47 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-64-1677 
         162         1216         1970         2696         1445          628 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1686         1126         1959           62         1305          864 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 
         866          610          573          385          174          422 
TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 
         202          690          414          165          230           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 
          89          382          100           77          129           61 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 
        1600          711          912          467          164           38 
TCGA-73-7498 TCGA-73-A9RS TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7147 
         621          305         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          505          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-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
         830           84          121          553          605          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-97-8179 TCGA-97-8547 
         107          182         1965           87           15          148 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
         115          197          271          427          459           44 
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-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
         116          266          312          111          102          827 
TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA 
          84         1951         1954         1954         1980         1951 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
        1970         1970          142         1971         1490          121 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                  1 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              6443               2696 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             513.5              471.5 
[1] "2.0 - 6443.0 (513.5)" "1.0 - 2696.0 (471.5)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  20P LOSS MUTATED         2       20       29        10        18         22
  20P LOSS WILD-TYPE       3       96      103        39        52         46
                    vv
clus                 STAGE IIIB STAGE IV
  20P LOSS MUTATED            4        6
  20P LOSS WILD-TYPE          7       18
D76V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 20                 96
  STAGE IB                 29                103
  STAGE IIA                10                 39
  STAGE IIB                18                 52
  STAGE IIIA               22                 46
  STAGE IIIB                4                  7
  STAGE IV                  6                 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
  20P LOSS MUTATED    28  64  11   6
  20P LOSS WILD-TYPE 119 203  31  12
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1               28                119
  T2               64                203
  T3               11                 31
  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    65  21    24
  20P LOSS WILD-TYPE 236  70    50
D76V5, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                  65                236
  N1                  21                 70
  N2+N3               24                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  20P LOSS MUTATED    82   6   0   0  23
  20P LOSS WILD-TYPE 244  12   1   4 100
D76V6, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                82                244
  M1                 6                 12
  M1A                0                  1
  M1B                0                  4
  MX                23                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"
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    60  51
  20P LOSS WILD-TYPE 195 170
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     60   51
  20P LOSS WILD-TYPE  195  170
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               60                195
  MALE                 51                170
[1] 2 2
[1] FALSE
D76V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20P LOSS MUTATED                            3
  20P LOSS WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20P LOSS MUTATED                                  26
  20P LOSS WILD-TYPE                                68
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                   70
  20P LOSS WILD-TYPE                                                233
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20P LOSS MUTATED                                            0
  20P LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20P LOSS MUTATED                                               6
  20P LOSS WILD-TYPE                                            13
                    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                             1
  20P LOSS WILD-TYPE                            2                            18
                    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                                             4
                    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)               70
  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                                     1
  LUNG SIGNET RING ADENOCARCINOMA                                   0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                     1
  MUCINOUS (COLLOID) CARCINOMA                                      1
                                                    clus
vv                                                   20P LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                233
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                      13
  LUNG CLEAR CELL ADENOCARCINOMA                                      0
  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"
D76V10, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     4 107
  20P LOSS WILD-TYPE  17 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4  107
  20P LOSS WILD-TYPE   17  348
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 4                 17
  YES              107                348
[1] 2 2
[1] FALSE
D76V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    80   3   1   4
  20P LOSS WILD-TYPE 247   9   3  17
D76V12, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               80                247
  R1                3                  9
  R2                1                  3
  RX                4                 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
  20P LOSS MUTATED                                  0     1
  20P LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           4    88
  20P LOSS WILD-TYPE                        31   279
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                       4                 31
  WHITE                                          88                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"
D76V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  79
  20P LOSS WILD-TYPE   6 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   79
  20P LOSS WILD-TYPE    6  266
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  6
  NOT HISPANIC OR LATINO               79                266
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    42  12
  20Q LOSS WILD-TYPE 287  75
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                54                362 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                12                 75 
$`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-44-3918 TCGA-44-3919 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
        1280         1036          190          466          287          351 
TCGA-49-4501 TCGA-49-6743 TCGA-49-6745 TCGA-50-5051 TCGA-50-5072 TCGA-53-7624 
        1421          369          522          455          246         1986 
TCGA-53-A4EZ TCGA-55-1595 TCGA-55-7283 TCGA-55-8087 TCGA-55-8090 TCGA-55-8097 
         280         1479           35          462            6           15 
TCGA-55-8207 TCGA-62-8397 TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
          66         1289         2067          910         1728         1189 
TCGA-67-3770 TCGA-67-3773 TCGA-67-6216 TCGA-69-7761 TCGA-69-A59K TCGA-73-4675 
          31          427          141          186          214           40 
TCGA-73-7499 TCGA-78-7146 TCGA-78-7158 TCGA-78-7160 TCGA-78-7537 TCGA-86-6851 
         519         1988         1963          678         1944         1959 
TCGA-86-7953 TCGA-86-8280 TCGA-86-8358 TCGA-91-6828 TCGA-91-6831 TCGA-93-7347 
         591           16           19          323          310          297 
TCGA-97-8174 TCGA-99-7458 TCGA-99-8033 TCGA-MP-A4SW TCGA-MP-A4TC TCGA-MP-A4TI 
        1965          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-44-4112 TCGA-44-5643 
          97          246         1130         1163          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-44-6775 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-44-8119 
        1970          882          535          719          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
         260          486          337          415           76         1932 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1081          428          999          268          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6761 TCGA-49-AARQ TCGA-50-5045 
        1700          445          890          354         6443         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-55-7284 TCGA-55-7570 
        1233         2151         1170           18          121            6 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
           4           95           40          705           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-55-8089 
          21            3           31            5           33          100 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 
         600           26            4           47           33           46 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
         674          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-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7031 TCGA-78-7145 
         305         1970         1967         1956         1965         1973 
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-78-7159 TCGA-78-7161 TCGA-78-7162 
        1948         1957         1961         1221          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-78-7539 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-86-7954 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-86-8281 TCGA-86-8359 TCGA-86-8585 
         489          476          482         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-91-6829 TCGA-91-6830 
          10           30           14           39         1940           60 
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          505          174           36           44          218 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 
         127          186           34            2         1973          568 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
         377          477          476          830           84          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
         553          605          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-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         427          459           44          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-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
         266          312          111          102          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
          84         1946         1951         1954         1954         1957 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        1980         1951         1970         1970          142         1971 
TCGA-MP-A5C7 TCGA-S2-AA1A 
        1490          121 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                  1 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2067               6443 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             492.5              476.0 
[1] "6.0 - 2067.0 (492.5)" "1.0 - 6443.0 (476.0)"
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  20Q LOSS MUTATED         0       12       23         8         5         11
  20Q LOSS WILD-TYPE       5      104      109        41        65         57
                    vv
clus                 STAGE IIIB STAGE IV
  20Q LOSS MUTATED            2        4
  20Q LOSS WILD-TYPE          9       20
D77V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  5
  STAGE IA                 12                104
  STAGE IB                 23                109
  STAGE IIA                 8                 41
  STAGE IIB                 5                 65
  STAGE IIIA               11                 57
  STAGE IIIB                2                  9
  STAGE IV                  4                 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
  20Q LOSS MUTATED    17  38   5   4
  20Q LOSS WILD-TYPE 130 229  37  14
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1               17                130
  T2               38                229
  T3                5                 37
  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    12
  20Q LOSS WILD-TYPE 258  83    62
D77V5, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                  43                258
  N1                   8                 83
  N2+N3               12                 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
  20Q LOSS MUTATED    51   4   0   0  10
  20Q LOSS WILD-TYPE 275  14   1   4 113
D77V6, multiclass
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                51                275
  M1                 4                 14
  M1A                0                  1
  M1B                0                  4
  MX                10                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"
D77V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    35  30
  20Q LOSS WILD-TYPE 220 191
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     35   30
  20Q LOSS WILD-TYPE  220  191
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               35                220
  MALE                 30                191
[1] 2 2
[1] FALSE
D77V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  20Q LOSS MUTATED                            3
  20Q LOSS WILD-TYPE                         12
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  20Q LOSS MUTATED                                  17
  20Q LOSS WILD-TYPE                                77
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q LOSS MUTATED                                                   34
  20Q LOSS WILD-TYPE                                                269
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  20Q LOSS MUTATED                                            0
  20Q LOSS WILD-TYPE                                          5
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  20Q LOSS MUTATED                                               4
  20Q LOSS WILD-TYPE                                            15
                    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                                             4
                    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                     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                                                   20Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                         12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                269
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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                       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"
D77V10, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1  64
  20Q LOSS WILD-TYPE  20 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   64
  20Q LOSS WILD-TYPE   20  391
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 1                 20
  YES               64                391
[1] 2 2
[1] FALSE
D77V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED    48   1   1   3
  20Q LOSS WILD-TYPE 279  11   3  18
D77V12, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               48                279
  R1                1                 11
  R2                1                  3
  RX                3                 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
  20Q LOSS MUTATED                                  0     1
  20Q LOSS WILD-TYPE                                1     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           1    52
  20Q LOSS WILD-TYPE                        34   315
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                 34
  WHITE                                          52                315
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2  45
  20Q LOSS WILD-TYPE   5 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2   45
  20Q LOSS WILD-TYPE    5  300
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO               45                300
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   109  32
  21Q LOSS WILD-TYPE 220  55
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               141                275 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                32                 55 
$`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          705           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-73-A9RS TCGA-75-7027 TCGA-75-7031 
         467          131           40          305         1956         1965 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 TCGA-78-7159 TCGA-78-7167 
        1988         1944          760         1948         1221         1937 
TCGA-78-7220 TCGA-78-7536 TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 TCGA-86-7701 
        1965         1949         1949         1954         1972           11 
TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
         422          591          745           26           35           34 
TCGA-91-6828 TCGA-91-6840 TCGA-91-7771 TCGA-95-7043 TCGA-95-7562 TCGA-95-8494 
         323          372          492            2         1973           84 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-99-8025 
         605         1965          182         1965           87          427 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AE TCGA-L9-A8F4 TCGA-MN-A4N4 
         459           44          170          282          102         1175 
TCGA-MP-A4SV TCGA-MP-A4TE TCGA-MP-A4TF 
        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-49-AARQ TCGA-50-5049 TCGA-50-5055 
         445          369          890         6443         2146          785 
TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5941 TCGA-50-5942 TCGA-50-6597 
         944          282          267          567          883         1015 
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-55-6980 TCGA-55-6987 TCGA-55-7281 
         993           24         1239           67         1170           18 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 
          35          121            6            4           95           39 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 TCGA-55-7914 TCGA-55-7995 
          39           34           19           16            3            5 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
          33          462          600            4           47           15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
          46           66          674          216           44           29 
TCGA-55-8506 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 
          11            9            3          146          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-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 
          29            1           28            5          162         1216 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
        1289         1970         2696         2067         2199          910 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 
        1728         1189         1126         1968         1305          864 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
         866          610          573          427          385          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
         141          422          690          414          165          230 
TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 
          70          100           77          214           61          912 
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-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 
        1973         1950         1093         1963         1202         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        1961         1963          678          215         1940         1950 
TCGA-78-7166 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        1934         1972         1944          327          881         1952 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5607 TCGA-83-5908 
         994         1971         1981         1964         1965          824 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
        1959          630         1968         1963          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-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 
         482           16         1955           19           45           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-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
         842          224           35          505          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-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
         568          377          477          476          830          121 
TCGA-95-A4VN TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         553          964         1932         1332          775          181 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
          22          107          147           15          148          115 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         197          271          392          154          114          287 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
         238          578          435          116            6          266 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 
         312          111          827           84         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-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
         142         1955         1971         1490          121 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                  1 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              2370               6443 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               591                448 
[1] "2.0 - 2370.0 (591.0)" "1.0 - 6443.0 (448.0)"
[1] "hr=" "1.1"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  21Q LOSS MUTATED         2       34       43        13        26         24
  21Q LOSS WILD-TYPE       3       82       89        36        44         44
                    vv
clus                 STAGE IIIB STAGE IV
  21Q LOSS MUTATED            5        7
  21Q LOSS WILD-TYPE          6       17
D78V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   2                  3
  STAGE IA                 34                 82
  STAGE IB                 43                 89
  STAGE IIA                13                 36
  STAGE IIB                26                 44
  STAGE IIIA               24                 44
  STAGE IIIB                5                  6
  STAGE IV                  7                 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
  21Q LOSS MUTATED    41  91  14   6
  21Q LOSS WILD-TYPE 106 176  28  12
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               41                106
  T2               91                176
  T3               14                 28
  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    99  28    24
  21Q LOSS WILD-TYPE 202  63    50
D78V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                  99                202
  N1                  28                 63
  N2+N3               24                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A M1B  MX
  21Q LOSS MUTATED   109   7   0   0  37
  21Q LOSS WILD-TYPE 217  11   1   4  86
D78V6, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               109                217
  M1                 7                 11
  M1A                0                  1
  M1B                0                  4
  MX                37                 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"
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    74  80
  21Q LOSS WILD-TYPE 181 141
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     74   80
  21Q LOSS WILD-TYPE  181  141
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               74                181
  MALE                 80                141
[1] 2 2
[1] FALSE
D78V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  21Q LOSS MUTATED                            8
  21Q LOSS WILD-TYPE                          7
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  21Q LOSS MUTATED                                  24
  21Q LOSS WILD-TYPE                                70
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                  107
  21Q LOSS WILD-TYPE                                                196
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  21Q LOSS MUTATED                                            0
  21Q LOSS WILD-TYPE                                          5
                    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                                             2
                    vv
clus                 MUCINOUS (COLLOID) CARCINOMA
  21Q LOSS MUTATED                              3
  21Q LOSS WILD-TYPE                            4
D78V9, multiclass
                                                    clus
vv                                                   21Q LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                        8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              107
  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                                          7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                196
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          5
  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                       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"
D78V10, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    10 144
  21Q LOSS WILD-TYPE  11 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     10  144
  21Q LOSS WILD-TYPE   11  311
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                10                 11
  YES              144                311
[1] 2 2
[1] FALSE
D78V11, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED   104   2   1   5
  21Q LOSS WILD-TYPE 223  10   3  16
D78V12, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              104                223
  R1                2                 10
  R2                1                  3
  RX                5                 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
  21Q LOSS MUTATED                                  1     1
  21Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          14   111
  21Q LOSS WILD-TYPE                        21   256
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                      14                 21
  WHITE                                         111                256
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     2 107
  21Q LOSS WILD-TYPE   5 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2  107
  21Q LOSS WILD-TYPE    5  238
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  5
  NOT HISPANIC OR LATINO              107                238
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   143  34
  22Q LOSS WILD-TYPE 186  53
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               177                239 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                34                 53 
$`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-73-A9RS TCGA-75-6214 TCGA-75-7027 
         467          131           38          305         1970         1956 
TCGA-75-7031 TCGA-78-7145 TCGA-78-7146 TCGA-78-7152 TCGA-78-7159 TCGA-78-7163 
        1965         1973         1988         1202         1221         1950 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-8640 TCGA-78-8660 TCGA-80-5608 
        1937         1972         1949         1949         1954         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 
         824         1959          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-95-7562 TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VN 
          44           34         1973          568           84          553 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 
         605          964         1932          775          181           87 
TCGA-97-8547 TCGA-99-7458 TCGA-99-8032 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A444 
         148          392           44          238          578            6 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T8 
         111          102           84         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-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
         369          522         6443         2174         2146          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5942 TCGA-50-5944 
         944         1499          246          267          883          764 
TCGA-50-5946 TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
         686          105         1971          701         1178         1479 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6983 TCGA-55-6986 
        1375            2           24         1239         1826         2151 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        1170          121            4          705           39           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7914 TCGA-55-7994 
          34           24           54           16            3           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           5           33          462          100            6          600 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          47           15           46          674          216           44 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8619 
          23           11          146          202          536           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 
         106           33           42         1952            1            5 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V 
        1216         1289         1970         2696         1445         2199 
TCGA-62-A471 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 
        1246         1189         1126           62          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-69-7765 TCGA-69-7974 TCGA-69-8254 TCGA-69-8255 TCGA-73-4658 TCGA-73-4666 
         165          184           77          129         1600          800 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-75-7025 TCGA-78-7147 
          40          164          621          519         1967         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
        1944         1093         1963          760         1948         1957 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 
        1961         1963          678          215         1940         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-78-8662 TCGA-80-5607 TCGA-86-7701 TCGA-86-7713 
        1971         1981         1964         1965           11          422 
TCGA-86-7714 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
        1968          508           10           13          489          476 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
          16         1955           45           18          455          405 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 
          10           14           39           79          842          224 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
          35          505          174          218          297          127 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
         186            2          377          477          476          830 
TCGA-95-A4VK TCGA-97-7547 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
         121         1965         1332           22          107          182 
TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
        1965          147           15          115          197          271 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         427          459          170          154          114          287 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 TCGA-MN-A4N1 
         282          435          116          266          312          827 
TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC 
        1175         1967         1954         1954         1980         1944 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
         142         1955         1971         1490          121 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                  1 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              2370               6443 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               479                476 
[1] "3.0 - 2370.0 (479.0)" "1.0 - 6443.0 (476.0)"
[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       55        21        32         32
  22Q LOSS WILD-TYPE       2       72       77        28        38         36
                    vv
clus                 STAGE IIIB STAGE IV
  22Q LOSS MUTATED            6       10
  22Q LOSS WILD-TYPE          5       14
D79V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   3                  2
  STAGE IA                 44                 72
  STAGE IB                 55                 77
  STAGE IIA                21                 28
  STAGE IIB                32                 38
  STAGE IIIA               32                 36
  STAGE IIIB                6                  5
  STAGE IV                 10                 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
  22Q LOSS MUTATED    61 116  18   8
  22Q LOSS WILD-TYPE  86 151  24  10
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               61                 86
  T2              116                151
  T3               18                 24
  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   127  40    34
  22Q LOSS WILD-TYPE 174  51    40
D79V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                 127                174
  N1                  40                 51
  N2+N3               34                 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
  22Q LOSS MUTATED   143   7   0   3  48
  22Q LOSS WILD-TYPE 183  11   1   1  75
D79V6, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               143                183
  M1                 7                 11
  M1A                0                  1
  M1B                3                  1
  MX                48                 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"
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    99 104
  22Q LOSS WILD-TYPE 156 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     99  104
  22Q LOSS WILD-TYPE  156  117
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               99                156
  MALE                104                117
[1] 2 2
[1] FALSE
D79V8, continuous
                    vv
clus                 LUNG ACINAR ADENOCARCINOMA
  22Q LOSS MUTATED                            9
  22Q LOSS WILD-TYPE                          6
                    vv
clus                 LUNG ADENOCARCINOMA MIXED SUBTYPE
  22Q LOSS MUTATED                                  36
  22Q LOSS WILD-TYPE                                58
                    vv
clus                 LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                  131
  22Q LOSS WILD-TYPE                                                172
                    vv
clus                 LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  22Q LOSS MUTATED                                            1
  22Q LOSS WILD-TYPE                                          4
                    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                                               4
  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                                        9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                36
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              131
  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                     4
  MUCINOUS (COLLOID) CARCINOMA                                      2
                                                    clus
vv                                                   22Q LOSS WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                          6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                  58
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                172
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                          4
  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     8 195
  22Q LOSS WILD-TYPE  13 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      8  195
  22Q LOSS WILD-TYPE   13  260
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 8                 13
  YES              195                260
[1] 2 2
[1] FALSE
D79V11, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED   139   5   1   7
  22Q LOSS WILD-TYPE 188   7   3  14
D79V12, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0              139                188
  R1                5                  7
  R2                1                  3
  RX                7                 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
  22Q LOSS MUTATED                                  1     1
  22Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          15   155
  22Q LOSS WILD-TYPE                        20   212
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                      15                 20
  WHITE                                         155                212
[1] 4 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     3 149
  22Q LOSS WILD-TYPE   4 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3  149
  22Q LOSS WILD-TYPE    4  196
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  4
  NOT HISPANIC OR LATINO              149                196
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    44  11
  XQ LOSS WILD-TYPE 285  76
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               55               361 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               11                76 
$`XQ LOSS MUTATED`
TCGA-05-4396 TCGA-05-4405 TCGA-05-5428 TCGA-05-5715 TCGA-35-4123 TCGA-44-5643 
        1947          610          670           62          182         1013 
TCGA-44-6146 TCGA-44-8120 TCGA-49-4507 TCGA-50-5066 TCGA-50-5932 TCGA-50-6597 
         302          260          268          944         1091         1015 
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-73-A9RS TCGA-78-7146 TCGA-78-7166 
         230          131          519          305         1988         1934 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7542 TCGA-78-8655 TCGA-86-7954 TCGA-86-7955 
        1965         1949         1952         1981         1963          508 
TCGA-86-8054 TCGA-86-8281 TCGA-86-8359 TCGA-91-8496 TCGA-95-7039 TCGA-95-7567 
         745         1955           26          505           34          568 
TCGA-95-8039 TCGA-95-8494 TCGA-97-8172 TCGA-97-8547 TCGA-97-A4M7 TCGA-L9-A50W 
         830           84          182          148          271          266 
TCGA-MP-A4TK 
        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-35-5375 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-38-4631 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-44-2662 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-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
         328          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-44-7671 TCGA-44-7672 
         218          557         1970          882          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-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-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARQ TCGA-50-5045 
         369          890          522          354         6443         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-50-7109 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-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
        2151         1170           18           35          121            4 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          95          705           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-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 
           5           33          462          100          600           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-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
         674          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-A490 TCGA-55-A492 TCGA-55-A493 
         106           33           42           48            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
           5           47         1216         1970         2696         1445 
TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
        2199         1246         1728          628         1189         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
        1126         1968         1959           62          864         1559 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
          31          610          385          174          141          422 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
         202          186          690          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-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
          61         1600          711          912          800          467 
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-78-7147 TCGA-78-7148 TCGA-78-7149 
        1956         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-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
        1937         1972         1944          327          881          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-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
         824         1959           11          630          422         1968 
TCGA-86-7953 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
         591           10         1963           13           24          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 
         489          476          482           16           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-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-91-6847 
          60          310           79          417          372          842 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
         224           35          492          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 
         218          297          127          186            2         1973 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
         377          477          476          121          553          605 
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-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
          22          107         1965           87          147           15 
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-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV 
         578          435          116            6          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         102          827         1175           84         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 
TCGA-S2-AA1A 
         121 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6                 1 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2067              6443 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              573               459 
[1] "6.0 - 2067.0 (573.0)" "1.0 - 6443.0 (459.0)"
[1] "hr=" "1.2"
D80V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA
  XQ LOSS MUTATED         0       13       17         3        13          8
  XQ LOSS WILD-TYPE       5      103      115        46        57         60
                   vv
clus                STAGE IIIB STAGE IV
  XQ LOSS MUTATED            3        2
  XQ LOSS WILD-TYPE          8       22
D80V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  0                 5
  STAGE IA                13               103
  STAGE IB                17               115
  STAGE IIA                3                46
  STAGE IIB               13                57
  STAGE IIIA               8                60
  STAGE IIIB               3                 8
  STAGE IV                 2                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
  XQ LOSS MUTATED    16  34   7   2
  XQ LOSS WILD-TYPE 131 233  35  16
D80V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              16               131
  T2              34               233
  T3               7                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
  XQ LOSS MUTATED    35  13     9
  XQ LOSS WILD-TYPE 266  78    65
D80V5, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0                 35               266
  N1                 13                78
  N2+N3               9                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
  XQ LOSS MUTATED    46   2   0   0  11
  XQ LOSS WILD-TYPE 280  16   1   4 112
D80V6, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               46               280
  M1                2                16
  M1A               0                 1
  M1B               0                 4
  MX               11               112
[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    25  34
  XQ LOSS WILD-TYPE 230 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     25   34
  XQ LOSS WILD-TYPE  230  187
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              25               230
  MALE                34               187
[1] 2 2
[1] FALSE
D80V8, continuous
                   vv
clus                LUNG ACINAR ADENOCARCINOMA
  XQ LOSS MUTATED                            3
  XQ LOSS WILD-TYPE                         12
                   vv
clus                LUNG ADENOCARCINOMA MIXED SUBTYPE
  XQ LOSS MUTATED                                  20
  XQ LOSS WILD-TYPE                                74
                   vv
clus                LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                   29
  XQ LOSS WILD-TYPE                                                274
                   vv
clus                LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  XQ LOSS MUTATED                                            0
  XQ LOSS WILD-TYPE                                          5
                   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                                             5
                   vv
clus                MUCINOUS (COLLOID) CARCINOMA
  XQ LOSS MUTATED                              1
  XQ LOSS WILD-TYPE                            6
D80V9, multiclass
                                                    clus
vv                                                   XQ LOSS MUTATED
  LUNG ACINAR ADENOCARCINOMA                                       3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                               20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              29
  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                                        12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                 74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               274
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                         5
  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                      5
  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  54
  XQ LOSS WILD-TYPE  16 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      5   54
  XQ LOSS WILD-TYPE   16  401
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                5                16
  YES              54               401
[1] 2 2
[1] FALSE
D80V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    39   0   0   2
  XQ LOSS WILD-TYPE 288  12   4  19
D80V12, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              39               288
  R1               0                12
  R2               0                 4
  RX               2                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
  XQ LOSS MUTATED                                  0     2
  XQ LOSS WILD-TYPE                                1     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           7    43
  XQ LOSS WILD-TYPE                        28   324
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                      7                28
  WHITE                                         43               324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  47
  XQ LOSS WILD-TYPE   7 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   47
  XQ LOSS WILD-TYPE    7  298
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 7
  NOT HISPANIC OR LATINO              47               298
[1] 2 2
[1] FALSE
