[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"        "-oTSTAD-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/STAD-TP/11541908/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/11549119/transformed.cor.cli.txt"

nPatients in clinical file=397, in cluster file=441, common to both=395
[1] "Reduce the number of clustering variables from 80 to 79."
[1]  79 395
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               46               349 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               46               349 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               91               304 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               91               304 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               69               326 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               69               326 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               59               336 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               59               336 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               48               347 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               48               347 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               86               309 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               86               309 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               18               377 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               18               377 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               381 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               381 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               90               305 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               90               305 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               36               359 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               36               359 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               69               326 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               69               326 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               55               340 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               55               340 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              174               221 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              174               221 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              151               244 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              151               244 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              166               229 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              166               229 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              214               181 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              214               181 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               54               341 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               54               341 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               67               328 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               67               328 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                92                303 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                92                303 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                66                329 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                66                329 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                56                339 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                56                339 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                65                330 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                65                330 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                79                316 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                79                316 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                69                326 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                69                326 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               138                257 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               138                257 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                373 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                22                373 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                35                360 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                35                360 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                51                344 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                51                344 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                41                354 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                41                354 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                24                371 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                24                371 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                51                344 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                51                344 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                78                317 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                78                317 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                51                344 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                51                344 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                48                347 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                48                347 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                66                329 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                66                329 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               215                180 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               215                180 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               248                147 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               248                147 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                374 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                374 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                364 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                31                364 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               51               344 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               51               344 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               51               344 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               51               344 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               370 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               370 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               25               370 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               25               370 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               29               366 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               29               366 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               76               319 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               76               319 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               44               351 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               44               351 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              147               248 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              147               248 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              145               250 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              145               250 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               50               345 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               50               345 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               90               305 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               90               305 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               49               346 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               49               346 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               62               333 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               62               333 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               377 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               18               377 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               29               366 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               29               366 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               72               323 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               72               323 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               26               369 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               26               369 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              125               270 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              125               270 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               88               307 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               88               307 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                54                341 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                54                341 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                57                338 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                57                338 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                55                340 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                55                340 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                51                344 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                51                344 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                54                341 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                54                341 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                43                352 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                43                352 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                35                360 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                35                360 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               100                295 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               100                295 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                84                311 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                84                311 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                90                305 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                90                305 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               101                294 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               101                294 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               143                252 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               143                252 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                69                326 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                69                326 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               101                294 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               101                294 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               133                262 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               133                262 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               100                295 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               100                295 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                77                318 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                77                318 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                20                375 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                20                375 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               154                241 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               154                241 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               125                270 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               125                270 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               42               353 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               42               353 
[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] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 395 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
         171          356           NA           NA           NA           NA 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4257 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-4292 TCGA-BR-4294 TCGA-BR-4357 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4361 TCGA-BR-4362 TCGA-BR-4363 TCGA-BR-4366 TCGA-BR-4367 TCGA-BR-4368 
          NA           NA           NA           NA           NA           NA 
TCGA-BR-4369 TCGA-BR-4370 TCGA-BR-4371 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 
          NA           NA           NA         1055          485           NA 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
         399          308          416          213         1190           25 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
          19          997          421          402          491           38 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
         273          642          940          949         1002          390 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
         280          753         1072          728          469          852 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
          21            5          564          378           29           21 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
         388          569          532           25           40           21 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
         373           15          625           22            8          394 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
           8          496           47           45          225          188 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
         593           11           NA          675           90           29 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
         418          131          427          101           11          583 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
         450           21            8          482          113          164 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
          22          280          615           34          389          481 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
          65          409            6          229           15          351 
TCGA-BR-8679 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
          NA          481          500           18          477           19 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
         325          382           35           20           92          677 
TCGA-BR-A4CR TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
          NA           28          408          411          392           24 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
          NA          431           16          390           20          589 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
         411           14          628          621           35          415 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
         352          156           86           99          400          401 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
           9            2           NA            2            2            2 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
           2            3            4            5            3            3 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
           4           NA            4            3          193            4 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
           4            4            4            2            3            3 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
           3           NA           92          822          485           NA 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4442 
         243          245         1645           NA           NA           NA 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4462 
         912         1431          580          366           NA           NA 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4474 TCGA-CG-4475 
          NA          577           NA          365           NA          699 
TCGA-CG-4476 TCGA-CG-4477 TCGA-CG-5716 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
          NA          942           NA           NA           31           31 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
          NA          183           30         3196           NA           NA 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
          NA         2405         1980          122         1674           NA 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
          NA          376          385          363          582          625 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
         573          564          566          543          181          523 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
         126          463          486          389          321          344 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
         375          752          511          593          523            7 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
         212          643          636          434          500          180 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
         461          419          449          417          342          344 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
          NA          297           90          476           NA          225 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
          NA           19          237          494          200          440 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
          NA          647          247           12          594           92 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
         678          519           NA           NA          413           17 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-7131 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
          47            7           NA           NA           NA           NA 
TCGA-HF-7136 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
          NA          550           NA           46           NA          434 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
         383          431          347          368          323           23 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
         739          170          374          360          736           99 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
         692          785          358          650          912          273 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
          NA          198          190          310            8           64 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
         394          589          538          374          294          270 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
         268          834          645           NA          572           NA 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
         559          163          158          398           NA          196 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
          NA          209          169           55           77          169 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
        1842          879           NA          600          131           NA 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
          NA           NA           NA         3720         1153         1236 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
        3519         3540         2171           NA           NA         1083 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
          NA          176           NA         1148           NA           NA 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
          NA          946           NA          680          723           NA 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK 
         580         1023           NA           NA           NA           NA 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
          NA           NA           NA           NA          587          717 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
        1964           NA         1800          873           NA          264 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
        1498           NA           NA          224          261           NA 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        1346          262           NA           NA           NA           NA 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        1219          912          642          128           NA 
Variable 1:'AGE':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=114,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=230,	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=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=27,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 395 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=53, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 21  87 173 104 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 21  87 173 104 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 21  87 173 104 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 21  87 173 104 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
122 107  75  79 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
122 107  75  79 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
122 107  75  79 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
122 107  75  79 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=7, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=33, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    25  15
  1P GAIN WILD-TYPE 217 107
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               40               324 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               15               107 
$`1P GAIN MUTATED`
TCGA-BR-4267 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8381 TCGA-BR-8483 
        6.18         0.69         0.95        12.95         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-CD-8535 
        0.72        12.79         0.62         0.72        13.51         0.13 
TCGA-CD-A48A TCGA-CG-4436 TCGA-D7-6521 TCGA-D7-6820 TCGA-D7-A4YU TCGA-D7-A6F0 
        0.13         7.99        18.54        11.31        16.44         2.96 
TCGA-EQ-8122 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4GF TCGA-HU-A4GH 
        7.79         1.55        26.47         5.92        25.81        11.77 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RO 
        8.98         6.25        12.95         3.45        18.38         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-KB-A6F7 TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
        6.44         6.74        60.56        16.67       115.69         8.94 
TCGA-VQ-A8DT TCGA-VQ-A8E2 TCGA-VQ-A8PK TCGA-VQ-A8PZ 
       37.74        31.10        17.85        59.18 

$`1P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.16        18.54        12.43         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49         0.82         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         0.72         0.26         0.26        16.31         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.48         7.40         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8382 
        3.32         0.36        19.17        14.79         0.69        15.85 
TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 
        3.72         9.21        20.22         1.12        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         0.59        15.68        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         0.79        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36         0.46        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         6.35         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.10         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
       29.98        47.05        19.07        12.03        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       18.97         7.07        12.00        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.84        18.61        17.85         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19         4.14        15.22        15.98        12.79        10.55 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
        6.97        21.14        20.91        14.27         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        9.76        15.65         4.34         7.40         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
       16.24         6.58        14.47        72.23        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39        19.53         3.02        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 
        5.03        13.58         0.56         0.23        18.08         1.51 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
        3.25        22.75        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        9.67         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT 
        3.39         5.36         5.19        13.08         6.87         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        1.81         2.53         5.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.31        11.05         8.61         4.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 
        5.79         0.92         5.46        13.25        13.02        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D 
       19.30        23.57        64.57        14.33        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
        8.68        49.25        20.81         1.71         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73        44.25         8.61        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        40.08        29.98        21.11         4.21         0.79 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.13              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           115.69            122.30 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            8.465            11.885 
[1] "0.1 - 115.7 (8.5)"  "0.1 - 122.3 (11.9)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         0        2        8        2         4         6
  1P GAIN WILD-TYPE       2       11       31       29        32        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           1          8          7          4        1
  1P GAIN WILD-TYPE         2         69         48         33       36
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                11
  STAGE IB                 8                31
  STAGE II                 2                29
  STAGE IIA                4                32
  STAGE IIB                6                43
  STAGE III                1                 2
  STAGE IIIA               8                69
  STAGE IIIB               7                48
  STAGE IIIC               4                33
  STAGE IV                 1                36
[1] 11  2
[1] TRUE
[1] "dimension of 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     5  10  22   7
  1P GAIN WILD-TYPE  16  77 151  97
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               5                16
  T2              10                77
  T3              22               151
  T4               7                97
[1] 4 2
[1] TRUE
[1] "dimension of 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    15  12   7   9
  1P GAIN WILD-TYPE 107  95  68  70
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              15               107
  N1              12                95
  N2               7                68
  N3               9                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  1P GAIN MUTATED    42   1   3
  1P GAIN WILD-TYPE 311  23  15
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              42               311
  M1               1                23
  MX               3                15
[1] 3 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    14  32
  1P GAIN WILD-TYPE 137 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     14   32
  1P GAIN WILD-TYPE  137  212
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              14               137
  MALE                32               212
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1P GAIN MUTATED                                       6
  1P GAIN WILD-TYPE                                    59
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                       22
  1P GAIN WILD-TYPE                                                    135
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                                   8
  1P GAIN WILD-TYPE                                                                61
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  1P GAIN MUTATED                                                  7
  1P GAIN WILD-TYPE                                               57
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  1P GAIN MUTATED                                                          0
  1P GAIN WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  1P GAIN MUTATED                                                           0
  1P GAIN WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  1P GAIN MUTATED                                          3
  1P GAIN WILD-TYPE                                        6
D1V8, multiclass
                                                                   clus
vv                                                                  1P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  1P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  46
  1P GAIN WILD-TYPE   6 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   46
  1P GAIN WILD-TYPE    6  343
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                 6
  YES              46               343
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    36   3   0   4
  1P GAIN WILD-TYPE 282  13  18  21
D1V10, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              36               282
  R1               3                13
  R2               0                18
  RX               4                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"
D1V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1P GAIN MUTATED      11                         0
  1P GAIN WILD-TYPE    77                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           0    32
  1P GAIN WILD-TYPE                                         1   211
D1V12, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  32               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"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    53  28
  1Q GAIN WILD-TYPE 189  94
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               81               283 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               28                94 
$`1Q GAIN MUTATED`
TCGA-BR-4267 TCGA-BR-6705 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8286 
        6.18        13.84         0.69        18.54         0.95        12.95 
TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 
        1.55         6.18        14.04         0.26         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8680 TCGA-BR-8687 
        9.21        20.22         1.12        12.79        15.81         0.62 
TCGA-BR-A452 TCGA-BR-A4J1 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66         0.72        12.82        13.51        20.42         1.15 
TCGA-CD-8524 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A48C TCGA-CD-A4MG 
        0.07         0.16         0.13         0.13         0.13         0.07 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4460 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 
        7.99        54.08        21.99        12.66        11.93        18.54 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.19         4.14        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-EQ-5647 
       24.72        19.50        16.44        11.31         2.96         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-8211 TCGA-FP-8631 
        7.79        72.23         0.39         3.02        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-A4GF 
        1.55        26.47         5.92        14.27        14.17        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4H2 TCGA-IN-7808 
       11.77         8.98         0.10         6.25        12.95         3.45 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
        1.41         6.44        60.56        16.67       115.69         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       35.61        37.74         5.46        31.10         2.70        17.85 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       14.33        59.18        28.70 

$`1Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.62        32.78        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 
       24.76        35.24        23.93        15.42        28.01         0.16 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        1.32         0.69        12.26         0.49        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 
        0.26         0.26        16.31         1.48         7.40        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
        4.31         3.32         0.36        19.17        14.79         0.69 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       15.85         3.72        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        16.44         0.59        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        12.56         1.15         3.02        22.26         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        14.17         0.53 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        19.36         0.46        20.65        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.10         6.35         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.13         0.10         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       27.02        15.95         1.02         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00        22.98        30.97         6.97         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       21.07         7.99        12.36        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8572 
       18.61        17.85         5.95        15.22        15.98        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19         0.23         6.97        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76        15.65         4.34         7.40         7.13 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
       16.24         6.58        14.47        21.27         8.12        19.53 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A8CX TCGA-HF-A5NB 
       22.29        17.06        59.54         5.03         0.23        18.08 
TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
        1.51        12.59        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       22.75        21.37        29.98         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        19.36        17.69        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        8.81        27.42        21.21        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
        5.36         5.19        13.08         6.74         6.87         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        1.81         2.53         5.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.31        11.05         8.61         4.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EB 
       40.64       116.38        71.38        57.44        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        0.92        13.25        13.02        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM 
        7.73        19.07        33.63        46.26        16.31         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        19.30        23.57        64.57 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W 
       11.70         8.68        49.25        20.81         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 
        8.58         9.73        44.25         8.61        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        6.58         5.72        40.08        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.07              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           115.69            122.30 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            11.31             11.70 
[1] "0.1 - 115.7 (11.3)" "0.1 - 122.3 (11.7)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         1        5       10        7         7         9
  1Q GAIN WILD-TYPE       1        8       29       24        29        40
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           1         18         15          7        6
  1Q GAIN WILD-TYPE         2         59         40         30       31
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 5                 8
  STAGE IB                10                29
  STAGE II                 7                24
  STAGE IIA                7                29
  STAGE IIB                9                40
  STAGE III                1                 2
  STAGE IIIA              18                59
  STAGE IIIB              15                40
  STAGE IIIC               7                30
  STAGE IV                 6                31
[1] 11  2
[1] TRUE
[1] "dimension of 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     7  20  43  19
  1Q GAIN WILD-TYPE  14  67 130  85
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               7                14
  T2              20                67
  T3              43               130
  T4              19                85
[1] 4 2
[1] TRUE
[1] "dimension of 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   28 19 20 19
  1Q GAIN WILD-TYPE 94 88 55 60
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              28                94
  N1              19                88
  N2              20                55
  N3              19                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  1Q GAIN MUTATED    79   5   7
  1Q GAIN WILD-TYPE 274  19  11
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              79               274
  M1               5                19
  MX               7                11
[1] 3 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    32  59
  1Q GAIN WILD-TYPE 119 185
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     32   59
  1Q GAIN WILD-TYPE  119  185
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              32               119
  MALE                59               185
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1Q GAIN MUTATED                                      11
  1Q GAIN WILD-TYPE                                    54
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                       37
  1Q GAIN WILD-TYPE                                                    120
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                                  14
  1Q GAIN WILD-TYPE                                                                55
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  1Q GAIN MUTATED                                                 22
  1Q GAIN WILD-TYPE                                               42
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  1Q GAIN MUTATED                                                          3
  1Q GAIN WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  1Q GAIN MUTATED                                                           1
  1Q GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  1Q GAIN MUTATED                                          3
  1Q GAIN WILD-TYPE                                        6
D2V8, multiclass
                                                                   clus
vv                                                                  1Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         37
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               22
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  1Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          120
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                55
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     2  89
  1Q GAIN WILD-TYPE   4 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   89
  1Q GAIN WILD-TYPE    4  300
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                2                 4
  YES              89               300
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    71   5   3   7
  1Q GAIN WILD-TYPE 247  11  15  18
D2V10, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              71               247
  R1               5                11
  R2               3                15
  RX               7                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"
D2V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1Q GAIN MUTATED      23                         2
  1Q GAIN WILD-TYPE    65                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           0    59
  1Q GAIN WILD-TYPE                                         1   184
D2V12, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                                  23                65
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  59               184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    43  21
  2P GAIN WILD-TYPE 199 101
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               64               300 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               21               101 
$`2P GAIN MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6566 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
        6.61        10.13        32.78         9.21        35.24        15.42 
TCGA-BR-7717 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 TCGA-BR-8362 TCGA-BR-8483 
        0.69         0.69         0.49         1.55         0.36         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-BR-A4PD 
        9.21        20.22         0.92        12.89        13.51        20.65 
TCGA-BR-A4PE TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CG-4460 
       20.42        13.15        13.18         0.30         0.07        21.99 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-6521 TCGA-D7-6815 
       12.00         1.02        12.03        79.07        18.54        15.98 
TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-HU-8249 TCGA-HU-8610 
        0.23        16.44        11.24        15.65        14.17         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4H0 
       24.30        12.30        22.75        25.81         8.98         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RO 
       12.95        17.69        12.30        27.42         3.45         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 
        6.74         6.87         5.56         5.56        28.90         4.31 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-AA68 
       31.10        21.73        17.85        20.81         1.71        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        21.11         4.21         0.79 

$`2P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.12        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
       12.76        18.71        17.49         0.82         1.32        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         0.72         0.26        12.95         0.26        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        1.48         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72         0.72         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
        1.15         0.66         3.02        22.26        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36         0.46         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        2.83         3.25         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       12.03         9.01        18.97         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.61        17.85         5.95        17.19         4.14 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74A 
       11.31        11.44         9.76         2.96         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.13         0.62         7.79        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27         8.12         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        1.55         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 
       14.27        12.59        11.41        12.10        10.62         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20         3.25        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
        0.10         6.51         6.25        10.19         0.26        19.36 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
        9.67         8.88         8.81        21.21        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NU 
       18.38         5.36         5.19        13.08         6.44         1.81 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
        2.53        60.56         3.72        19.73        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.67        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        37.74         5.46        13.25        13.02 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       19.30        23.57        64.57        14.33        59.18        28.70 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       11.70         8.68        49.25         7.36         8.58         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
       44.25         8.61        55.43         4.54         6.58         5.72 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            79.07            122.30 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           12.300            11.425 
[1] "0.1 - 79.1 (12.3)"  "0.1 - 122.3 (11.4)"
[1] "hr=" "1"  
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         0        5        5        7         7        10
  2P GAIN WILD-TYPE       2        8       34       24        29        39
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           1         12          7          8        6
  2P GAIN WILD-TYPE         2         65         48         29       31
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 5                 8
  STAGE IB                 5                34
  STAGE II                 7                24
  STAGE IIA                7                29
  STAGE IIB               10                39
  STAGE III                1                 2
  STAGE IIIA              12                65
  STAGE IIIB               7                48
  STAGE IIIC               8                29
  STAGE IV                 6                31
[1] 11  2
[1] TRUE
[1] "dimension of 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     5  11  35  17
  2P GAIN WILD-TYPE  16  76 138  87
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               5                16
  T2              11                76
  T3              35               138
  T4              17                87
[1] 4 2
[1] TRUE
[1] "dimension of 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   25 15 13 15
  2P GAIN WILD-TYPE 97 92 62 64
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              25                97
  N1              15                92
  N2              13                62
  N3              15                64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  2P GAIN MUTATED    63   4   2
  2P GAIN WILD-TYPE 290  20  16
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              63               290
  M1               4                20
  MX               2                16
[1] 3 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    27  42
  2P GAIN WILD-TYPE 124 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     27   42
  2P GAIN WILD-TYPE  124  202
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              27               124
  MALE                42               202
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  2P GAIN MUTATED                                       8
  2P GAIN WILD-TYPE                                    57
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                       26
  2P GAIN WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                                  14
  2P GAIN WILD-TYPE                                                                55
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  2P GAIN MUTATED                                                 16
  2P GAIN WILD-TYPE                                               48
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  2P GAIN MUTATED                                                          1
  2P GAIN WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  2P GAIN MUTATED                                                           3
  2P GAIN WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  2P GAIN MUTATED                                          0
  2P GAIN WILD-TYPE                                        9
D3V8, multiclass
                                                                   clus
vv                                                                  2P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  2P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                55
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  69
  2P GAIN WILD-TYPE   6 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   69
  2P GAIN WILD-TYPE    6  320
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                0                 6
  YES              69               320
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    62   0   3   2
  2P GAIN WILD-TYPE 256  16  15  23
D3V10, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              62               256
  R1               0                16
  R2               3                15
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2P GAIN MUTATED      21                         1
  2P GAIN WILD-TYPE    67                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           0    38
  2P GAIN WILD-TYPE                                         1   205
D3V12, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                                  21                67
  BLACK OR AFRICAN AMERICAN                               1                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  38               205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    35  19
  2Q GAIN WILD-TYPE 207 103
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               54               310 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               19               103 
$`2Q GAIN MUTATED`
TCGA-BR-6456 TCGA-BR-6566 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
       10.13        32.78         9.21        35.24        15.42         0.69 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8295 TCGA-BR-8362 TCGA-BR-8483 TCGA-BR-8485 
        0.69         0.49         1.55         0.36         5.39         9.21 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-CD-5801 
        0.92        12.89         0.66        13.51        20.42        13.18 
TCGA-CD-8524 TCGA-CD-A48C TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5724 
        0.07         0.13        21.99        12.00         1.02        12.03 
TCGA-CG-5727 TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-EQ-8122 
       79.07        18.54        15.98        16.44        11.24         7.79 
TCGA-F1-6875 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF TCGA-HU-A4H0 
       72.23         0.76        24.30        12.30        25.81         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-A6RR TCGA-IN-A6RS 
       12.95        17.69        12.30         3.45         6.74         6.87 
TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-VQ-A8E2 TCGA-VQ-A8PK 
        5.56         5.56        28.90         4.31        31.10        17.85 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       20.81         1.71        29.98        21.11         4.21         0.79 

$`2Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.12        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.62        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       23.93        28.01         0.16        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        0.69        12.76        18.71        17.49         0.82         1.32 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       12.26        20.55         0.72         0.26        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       16.31         1.48         7.40         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
       15.85         3.72         0.72        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         0.79         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
       12.82        19.36         0.46        20.65         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       11.57         5.13         2.83         3.25        13.15         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
        6.35         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98        30.97         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
        5.95        17.19         4.14        15.22        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
        0.23         6.97        21.14        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76         2.96        15.65         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        0.62        16.24         6.58        14.47        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39        19.53         3.02        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         1.55         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       11.41        12.10        10.62         5.59        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
        0.10         6.51         6.25        10.19         0.26        19.36 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        9.67         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO 
        3.39        18.38         5.36         5.19        13.08         1.41 
TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
        6.44         1.81         2.53        60.56         3.72        19.73 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         4.67        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        16.87         5.79         0.92        37.74         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        13.02        21.73        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       19.07        33.63        46.26        16.31         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        19.30        23.57        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        59.18        28.70        11.70         8.68        49.25 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         8.58         9.73        44.25         8.61        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
        4.54         6.58         5.72        40.08 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.07              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            79.07            122.30 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           11.620            11.635 
[1] "0.1 - 79.1 (11.6)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         0        4        4        5         6        10
  2Q GAIN WILD-TYPE       2        9       35       26        30        39
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           1          8          7          6        6
  2Q GAIN WILD-TYPE         2         69         48         31       31
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 4                 9
  STAGE IB                 4                35
  STAGE II                 5                26
  STAGE IIA                6                30
  STAGE IIB               10                39
  STAGE III                1                 2
  STAGE IIIA               8                69
  STAGE IIIB               7                48
  STAGE IIIC               6                31
  STAGE IV                 6                31
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED     3  10  31  14
  2Q GAIN WILD-TYPE  18  77 142  90
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               3                18
  T2              10                77
  T3              31               142
  T4              14                90
[1] 4 2
[1] TRUE
[1] "dimension of 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    20  14  10  13
  2Q GAIN WILD-TYPE 102  93  65  66
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              20               102
  N1              14                93
  N2              10                65
  N3              13                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  2Q GAIN MUTATED    51   4   4
  2Q GAIN WILD-TYPE 302  20  14
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              51               302
  M1               4                20
  MX               4                14
[1] 3 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    24  35
  2Q GAIN WILD-TYPE 127 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     24   35
  2Q GAIN WILD-TYPE  127  209
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              24               127
  MALE                35               209
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  2Q GAIN MUTATED                                       6
  2Q GAIN WILD-TYPE                                    59
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                       25
  2Q GAIN WILD-TYPE                                                    132
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                                  14
  2Q GAIN WILD-TYPE                                                                55
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  2Q GAIN MUTATED                                                 10
  2Q GAIN WILD-TYPE                                               54
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  2Q GAIN MUTATED                                                          1
  2Q GAIN WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  2Q GAIN MUTATED                                                           2
  2Q GAIN WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  2Q GAIN MUTATED                                          0
  2Q GAIN WILD-TYPE                                        9
D4V8, multiclass
                                                                   clus
vv                                                                  2Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  2Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                55
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  59
  2Q GAIN WILD-TYPE   6 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   59
  2Q GAIN WILD-TYPE    6  330
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                0                 6
  YES              59               330
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    51   0   3   2
  2Q GAIN WILD-TYPE 267  16  15  23
D4V10, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              51               267
  R1               0                16
  R2               3                15
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2Q GAIN MUTATED      15                         2
  2Q GAIN WILD-TYPE    73                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           0    34
  2Q GAIN WILD-TYPE                                         1   209
D4V12, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                                  15                73
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  34               209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    31  12
  3P GAIN WILD-TYPE 211 110
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               43               321 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               12               110 
$`3P GAIN MUTATED`
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-6802 TCGA-BR-7196 TCGA-BR-7722 
        6.18        34.68         0.62        30.90        12.82         0.16 
TCGA-BR-7901 TCGA-BR-8296 TCGA-BR-8373 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-CD-5799 
        0.95         1.48        14.79        19.36        20.65         3.25 
TCGA-CD-5801 TCGA-CD-8528 TCGA-CG-4444 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5727 
       13.18         0.10        47.05        30.97        12.03        79.07 
TCGA-D7-6815 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-F1-A448 TCGA-FP-7998 
       15.98        16.44        11.24         2.96        21.27        22.29 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 
       24.20        22.75        25.81         8.98         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8P5 
       19.36        12.30        27.42        35.61        37.74         7.73 
TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Y 
       17.85        23.41        64.57        59.18         8.68         9.73 
TCGA-VQ-A922 
        8.61 

$`3P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 
       18.35        30.90         9.57         6.61        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       10.13        13.68         7.00        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       31.20        32.94         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       15.42        28.01         0.69        18.54        12.43         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         0.49        20.55         0.72         0.26        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.26        16.31         1.55         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 
        4.31        14.04         3.32         0.36        19.17         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        0.59        15.68         0.62        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         0.79         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.66        13.51         0.46        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13         2.83        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         6.35 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 
       29.98        19.07        12.03        21.99         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        22.98         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85         5.95        17.19         4.14        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19         0.23         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       11.31        11.44         9.76        15.65         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.13         0.62         7.79        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 
       72.23         8.12         0.39        19.53         3.02        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       59.54         5.03        13.58         0.56         1.55         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ 
        5.59        12.30        11.84         3.25        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       17.69         9.67         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        1.41         6.44         6.74         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.31        11.05         8.61         4.67        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
        8.94        16.87         5.79         0.92         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
       13.02        31.10        21.73        22.36        23.77        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       33.63        46.26        16.31         2.70         1.87         9.27 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        19.30        23.57        14.33        28.70        11.70 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z 
       49.25        20.81         1.71         7.36         8.58        44.25 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B 
       55.43         4.54         6.58         5.72        40.08        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11         4.21         0.79 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.10              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            79.07            122.30 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            15.98             11.05 
[1] "0.1 - 79.1 (16.0)"  "0.1 - 122.3 (11.1)"
[1] "hr=" "1.7"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         0        2        5        4         4         8
  3P GAIN WILD-TYPE       2       11       34       27        32        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           0          7          6          6        5
  3P GAIN WILD-TYPE         3         70         49         31       32
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                11
  STAGE IB                 5                34
  STAGE II                 4                27
  STAGE IIA                4                32
  STAGE IIB                8                41
  STAGE III                0                 3
  STAGE IIIA               7                70
  STAGE IIIB               6                49
  STAGE IIIC               6                31
  STAGE IV                 5                32
[1] 11  2
[1] TRUE
[1] "dimension of 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     2  11  19  15
  3P GAIN WILD-TYPE  19  76 154  89
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               2                19
  T2              11                76
  T3              19               154
  T4              15                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P GAIN MUTATED    16  11   7  12
  3P GAIN WILD-TYPE 106  96  68  67
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              16               106
  N1              11                96
  N2               7                68
  N3              12                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  3P GAIN MUTATED    45   2   1
  3P GAIN WILD-TYPE 308  22  17
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              45               308
  M1               2                22
  MX               1                17
[1] 3 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    20  28
  3P GAIN WILD-TYPE 131 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     20   28
  3P GAIN WILD-TYPE  131  216
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              20               131
  MALE                28               216
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3P GAIN MUTATED                                       8
  3P GAIN WILD-TYPE                                    57
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                       15
  3P GAIN WILD-TYPE                                                    142
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                                  10
  3P GAIN WILD-TYPE                                                                59
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  3P GAIN MUTATED                                                 11
  3P GAIN WILD-TYPE                                               53
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3P GAIN MUTATED                                                          2
  3P GAIN WILD-TYPE                                                       19
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  3P GAIN MUTATED                                                           1
  3P GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3P GAIN MUTATED                                          1
  3P GAIN WILD-TYPE                                        8
D5V8, multiclass
                                                                   clus
vv                                                                  3P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  3P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          142
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  48
  3P GAIN WILD-TYPE   6 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   48
  3P GAIN WILD-TYPE    6  341
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                 6
  YES              48               341
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    40   1   2   4
  3P GAIN WILD-TYPE 278  15  16  21
D5V10, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              40               278
  R1               1                15
  R2               2                16
  RX               4                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"
D5V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED      14                         0
  3P GAIN WILD-TYPE    74                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           0    25
  3P GAIN WILD-TYPE                                         1   218
D5V12, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                                  14                74
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  25               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    55  24
  3Q GAIN WILD-TYPE 187  98
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               79               285 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               24                98 
$`3Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6565 TCGA-BR-6802 TCGA-BR-7196 
       11.70         6.18        34.68         0.62        30.90        12.82 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 
        0.16        18.54         0.95         0.72         1.55         1.48 
TCGA-BR-8361 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8589 
       19.50        13.74        14.79         0.72        12.79        15.81 
TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-5801 
        0.53        19.36        20.65        20.42         3.25        13.18 
TCGA-CD-5803 TCGA-CD-8527 TCGA-CD-8528 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4444 
        0.07         0.07         0.10        15.95         7.99        47.05 
TCGA-CG-4455 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-6521 
       12.03        12.00        30.97        12.03        79.07        18.54 
TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-F1-A448 
       15.98        24.72        16.44        11.24         2.96        21.27 
TCGA-FP-7916 TCGA-FP-7998 TCGA-HJ-7597 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GC 
        3.02        22.29        26.47        12.30        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
       22.75        25.81         8.98         2.10        12.95        19.36 
TCGA-HU-A4HD TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F7 TCGA-RD-A8MW 
       27.42         6.44         5.56         1.81        60.56        37.91 
TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
      115.69        35.61        37.74        13.02        31.10        21.73 
TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A8PX 
        7.73         2.70        17.85        23.41        23.57        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91E TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-AA6J 
       59.18         8.68         9.73         8.61         4.54        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`3Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
       30.90         9.57         6.61        15.95        13.12        10.13 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68         7.00        39.12         0.82        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6803 
       13.22        16.14         1.25         8.98        21.11        31.20 
TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       32.94         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       28.01         0.69        12.43         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49         0.82         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 
       20.55         0.26        12.95         0.26        16.31         7.40 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 
        4.31        14.04         3.32         0.36        19.17         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
        1.12         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.92        13.41        13.51        12.89         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PF 
       14.17        12.82         0.66        13.51         0.46         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 
       13.64        11.57         5.13         2.83        13.15         0.30 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.13         0.13         0.10         6.35         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4437 
        0.10        20.02         3.02        27.02         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 
       54.08         4.01        14.01        29.98        19.07        21.99 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
        9.01        18.97         7.07        22.98         6.97         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       28.96        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       18.61        17.85         5.95        17.19         4.14        15.22 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        11.31        12.33        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19         0.23         6.97        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
        5.92        15.16        13.78        14.76        13.71        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76        15.65         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        0.62         7.79        16.24         6.58        14.47        72.23 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        8.12         0.39        19.53        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 
       13.58         0.56         1.55         0.23        18.08         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GH 
       10.62         0.76        24.30         5.59        11.84        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       21.37        29.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
        0.26        17.69        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IP-7968 
        5.19        13.08         1.41         6.74         6.87         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
        5.56        28.90         3.72        19.73         4.31        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         4.67        16.67       122.30        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87         5.79         0.92 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
        5.46        13.25        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       46.26        16.31         1.87         9.27        15.65        19.30 
TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       14.33        28.70        11.70        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        7.36         8.58        44.25        55.43         6.58         5.72 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-ZA-A8F6 
       40.08        29.98         4.21 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.07              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           115.69            122.30 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            13.18             10.55 
[1] "0.1 - 115.7 (13.2)" "0.1 - 122.3 (10.6)"
[1] "hr=" "1.4"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         0        3       10        8         5        10
  3Q GAIN WILD-TYPE       2       10       29       23        31        39
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           0         12         16         12        8
  3Q GAIN WILD-TYPE         3         65         39         25       29
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                10
  STAGE IB                10                29
  STAGE II                 8                23
  STAGE IIA                5                31
  STAGE IIB               10                39
  STAGE III                0                 3
  STAGE IIIA              12                65
  STAGE IIIB              16                39
  STAGE IIIC              12                25
  STAGE IV                 8                29
[1] 11  2
[1] TRUE
[1] "dimension of 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     5  19  31  30
  3Q GAIN WILD-TYPE  16  68 142  74
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               5                16
  T2              19                68
  T3              31               142
  T4              30                74
[1] 4 2
[1] TRUE
[1] "dimension of 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   25 20 17 21
  3Q GAIN WILD-TYPE 97 87 58 58
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              25                97
  N1              20                87
  N2              17                58
  N3              21                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  3Q GAIN MUTATED    76   4   6
  3Q GAIN WILD-TYPE 277  20  12
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              76               277
  M1               4                20
  MX               6                12
[1] 3 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    33  53
  3Q GAIN WILD-TYPE 118 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     33   53
  3Q GAIN WILD-TYPE  118  191
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              33               118
  MALE                53               191
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3Q GAIN MUTATED                                      13
  3Q GAIN WILD-TYPE                                    52
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                       31
  3Q GAIN WILD-TYPE                                                    126
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                                  17
  3Q GAIN WILD-TYPE                                                                52
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  3Q GAIN MUTATED                                                 17
  3Q GAIN WILD-TYPE                                               47
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3Q GAIN MUTATED                                                          3
  3Q GAIN WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  3Q GAIN MUTATED                                                           1
  3Q GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3Q GAIN MUTATED                                          3
  3Q GAIN WILD-TYPE                                        6
D6V8, multiclass
                                                                   clus
vv                                                                  3Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  3Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     1  85
  3Q GAIN WILD-TYPE   5 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   85
  3Q GAIN WILD-TYPE    5  304
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                1                 5
  YES              85               304
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    71   2   5   5
  3Q GAIN WILD-TYPE 247  14  13  20
D6V10, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              71               247
  R1               2                14
  R2               5                13
  RX               5                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"
D6V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED      20                         2
  3Q GAIN WILD-TYPE    68                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           0    48
  3Q GAIN WILD-TYPE                                         1   195
D6V12, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                                  20                68
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  48               195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    14   4
  4P GAIN WILD-TYPE 228 118
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               18               346 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               118 
$`4P GAIN MUTATED`
TCGA-BR-8484 TCGA-BR-A4IY TCGA-CD-8528 TCGA-CG-4443 TCGA-CG-4475 TCGA-CG-5720 
        0.72        12.89         0.10        29.98        22.98         0.99 
TCGA-CG-5722 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-HU-A4GH 
        0.99        12.66        11.93        11.24        15.65        11.77 
TCGA-IN-7806 TCGA-IN-A7NT TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A91Q 
       21.21         5.56        17.85         1.87        23.57        20.81 

$`4P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.25         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01         0.69         0.16        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        0.69        12.76        18.71        17.49         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         0.26        16.31         1.55         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         0.59        15.68         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56         1.15         0.66         3.02        22.26         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51         0.79         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.82         0.66        19.36        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.13         0.13         0.10         6.35         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        7.99         8.05        54.08         4.01        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03        21.99         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 
       12.00        30.97         6.97         1.02         1.02         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 
        4.01        55.04        21.07         7.99        12.36        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.19         4.14        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
        0.23         6.97        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
        5.92        15.16        13.78        14.76        13.71        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         2.96         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        0.62         7.79        16.24         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27         8.12         0.39        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         1.55 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.23        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        17.69        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         6.44         6.74         6.87 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
        1.81         2.53         5.56        60.56        28.90         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       19.73         4.31        11.05         8.61         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       37.74         5.46        13.25        13.02        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       16.31         2.70         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       49.25         1.71         7.36         8.58         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
        8.61        55.43         4.54         6.58         5.72        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        21.11         4.21         0.79 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.10              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            29.98            122.30 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           12.295            11.490 
[1] "0.1 - 30.0 (12.3)"  "0.1 - 122.3 (11.5)"
[1] "hr=" "1.5"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         0        2        2        0         0         4
  4P GAIN WILD-TYPE       2       11       37       31        36        45
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           0          6          1          0        3
  4P GAIN WILD-TYPE         3         71         54         37       34
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                11
  STAGE IB                 2                37
  STAGE II                 0                31
  STAGE IIA                0                36
  STAGE IIB                4                45
  STAGE III                0                 3
  STAGE IIIA               6                71
  STAGE IIIB               1                54
  STAGE IIIC               0                37
  STAGE IV                 3                34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED     2   3   8   5
  4P GAIN WILD-TYPE  19  84 165  99
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               2                19
  T2               3                84
  T3               8               165
  T4               5                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P GAIN MUTATED     6   5   4   3
  4P GAIN WILD-TYPE 116 102  71  76
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               6               116
  N1               5               102
  N2               4                71
  N3               3                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  4P GAIN MUTATED    17   1   0
  4P GAIN WILD-TYPE 336  23  18
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0              17               336
  M1               1                23
  MX               0                18
[1] 3 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     5  13
  4P GAIN WILD-TYPE 146 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5   13
  4P GAIN WILD-TYPE  146  231
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               5               146
  MALE                13               231
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  4P GAIN MUTATED                                       1
  4P GAIN WILD-TYPE                                    64
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                        6
  4P GAIN WILD-TYPE                                                    151
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                                   3
  4P GAIN WILD-TYPE                                                                66
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  4P GAIN MUTATED                                                  5
  4P GAIN WILD-TYPE                                               59
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  4P GAIN MUTATED                                                          1
  4P GAIN WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  4P GAIN MUTATED                                                           0
  4P GAIN WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  4P GAIN MUTATED                                          1
  4P GAIN WILD-TYPE                                        8
D7V8, multiclass
                                                                   clus
vv                                                                  4P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  4P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  18
  4P GAIN WILD-TYPE   6 371
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   18
  4P GAIN WILD-TYPE    6  371
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                0                 6
  YES              18               371
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    16   1   1   0
  4P GAIN WILD-TYPE 302  15  17  25
D7V10, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              16               302
  R1               1                15
  R2               1                17
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4P GAIN MUTATED       3                         0
  4P GAIN WILD-TYPE    85                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0    10
  4P GAIN WILD-TYPE                                         1   233
D7V12, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                                   3                85
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  10               233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     8   6
  4Q GAIN WILD-TYPE 234 116
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               14               350 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                6               116 
$`4Q GAIN MUTATED`
TCGA-BR-8484 TCGA-CG-4475 TCGA-CG-5720 TCGA-CG-5722 TCGA-D7-5578 TCGA-D7-A6EV 
        0.72        22.98         0.99         0.99        12.66        11.24 
TCGA-HJ-7597 TCGA-HU-8249 TCGA-IN-7806 TCGA-RD-A8N5 TCGA-VQ-A8PK TCGA-VQ-A8PM 
       26.47        14.17        21.21        57.44        17.85         1.87 
TCGA-VQ-A8PU TCGA-VQ-A91Q 
       23.57        20.81 

$`4Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.25         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01         0.69         0.16        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        0.69        12.76        18.71        17.49         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         0.26        16.31         1.55         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         0.59        15.68         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       12.56         1.15         0.66         3.02        22.26         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         0.79         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
        0.53        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       20.65        20.42         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        2.83         3.25        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.35         0.13         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.10         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       15.95         1.02         7.99         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
       14.01        29.98        47.05        19.07        12.03        21.99 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        1.02         1.02         6.02       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.36        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85         5.95        17.19         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19         0.23         6.97 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.79        16.24         6.58        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
        8.12         0.39        19.53         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       59.54         5.03        13.58         0.56         1.55         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       18.08         1.51         5.92        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       12.30         9.67         8.88         8.81        27.42         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        1.41         6.44         6.74         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.31        11.05         8.61         4.67        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 
       37.91        40.64       115.69       116.38        71.38         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        16.87         5.79         0.92        37.74         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ 
        7.73        19.07        33.63        46.26        16.31         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        9.27        23.41        15.65        19.30        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U 
       59.18        28.70        11.70         8.68        49.25         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         8.58         9.73        44.25         8.61        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        4.54         6.58         5.72        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.72              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            57.44            122.30 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            16.01             11.49 
[1] "0.7 - 57.4 (16.0)"  "0.1 - 122.3 (11.5)"
[1] "hr=" "1.1"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         0        0        2        0         0         3
  4Q GAIN WILD-TYPE       2       13       37       31        36        46
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           0          5          1          0        3
  4Q GAIN WILD-TYPE         3         72         54         37       34
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                13
  STAGE IB                 2                37
  STAGE II                 0                31
  STAGE IIA                0                36
  STAGE IIB                3                46
  STAGE III                0                 3
  STAGE IIIA               5                72
  STAGE IIIB               1                54
  STAGE IIIC               0                37
  STAGE IV                 3                34
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   3   8   3
  4Q GAIN WILD-TYPE  21  84 165 101
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                21
  T2               3                84
  T3               8               165
  T4               3               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q GAIN MUTATED     2   5   4   3
  4Q GAIN WILD-TYPE 120 102  71  76
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               2               120
  N1               5               102
  N2               4                71
  N3               3                76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  4Q GAIN MUTATED    12   1   1
  4Q GAIN WILD-TYPE 341  23  17
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0              12               341
  M1               1                23
  MX               1                17
[1] 3 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     4  10
  4Q GAIN WILD-TYPE 147 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4   10
  4Q GAIN WILD-TYPE  147  234
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4               147
  MALE                10               234
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  4Q GAIN MUTATED                                       1
  4Q GAIN WILD-TYPE                                    64
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                        3
  4Q GAIN WILD-TYPE                                                    154
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                                   2
  4Q GAIN WILD-TYPE                                                                67
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  4Q GAIN MUTATED                                                  4
  4Q GAIN WILD-TYPE                                               60
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  4Q GAIN MUTATED                                                          1
  4Q GAIN WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  4Q GAIN MUTATED                                                           0
  4Q GAIN WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  4Q GAIN MUTATED                                          2
  4Q GAIN WILD-TYPE                                        7
D8V8, multiclass
                                                                   clus
vv                                                                  4Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          3
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               2
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  4Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          154
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                67
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 60
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0  14
  4Q GAIN WILD-TYPE   6 375
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   14
  4Q GAIN WILD-TYPE    6  375
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                 6
  YES              14               375
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    13   0   1   0
  4Q GAIN WILD-TYPE 305  16  17  25
D8V10, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              13               305
  R1               0                16
  R2               1                17
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4Q GAIN MUTATED       1                         0
  4Q GAIN WILD-TYPE    87                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0     9
  4Q GAIN WILD-TYPE                                         1   234
D8V12, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                                   1                87
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                   9               234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    55  28
  5P GAIN WILD-TYPE 187  94
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               83               281 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               28                94 
$`5P GAIN MUTATED`
TCGA-BR-4187 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7901 
        4.64        35.24        15.42        28.01         0.69         0.95 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
        1.32         0.69         0.72        12.95         0.26         1.48 
TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8486 
        0.26         2.96        13.74        14.79         9.21        20.22 
TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4PD TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8525 
       11.54         0.62        20.65        13.18         0.07         0.07 
TCGA-CD-8528 TCGA-CD-A486 TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 
        0.10         6.35         0.13         7.99        54.08        14.01 
TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       47.05        12.03        21.99        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5730 
       22.98         1.02         0.99        12.03        15.02         4.01 
TCGA-D7-5579 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
       11.93         4.14        15.22        10.55        11.31        24.72 
TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 
        6.97        11.31         2.96        15.65         0.62         7.79 
TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 
       19.53        17.06         0.23         1.51        12.59        14.17 
TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H0 TCGA-HU-A4H5 
       24.30         3.25        22.75        25.81         2.10        12.30 
TCGA-HU-A4HD TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-RD-A8N5 TCGA-RD-A8N6 
       27.42         5.56         1.81         5.56        57.44         8.94 
TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PK 
       35.61         5.46        13.25        31.10        21.73        17.85 
TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-AA68 TCGA-VQ-AA6J 
       28.70         8.58        44.25        40.08        21.11 

$`5P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         6.97         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
        9.21        24.76        23.93         0.16        18.54        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        0.69        12.76        18.71        17.49         0.82        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.49        20.55         0.26        16.31         1.55         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 
        6.18        19.50         0.36        22.19         0.95         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 
       14.04         3.32         0.36        19.17         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 
       15.85         3.72         5.39         0.72         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44         0.59        15.68        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
        1.15         0.66         3.02        22.26         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         0.79         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE 
       12.82         0.66        19.36        13.51         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
       13.15         0.30         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4477 
        8.05         4.01        29.98        19.07         9.01        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5726 
        6.97         1.02         0.99         6.02       105.07        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 
       17.85         5.95        17.19        15.98        12.79        12.33 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19         0.23        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       13.71        11.24        11.44         9.76         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.13        16.24         6.58        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        8.12         0.39         3.02        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56         1.55        18.08        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       14.27        11.41        12.10        10.62         0.76         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       12.30        11.84        24.20        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        17.69         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         6.44         6.74         6.87 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53        60.56        28.90         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         4.67        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EB 
       40.64       115.69       116.38        71.38        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
        0.92        37.74        13.02        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       19.07        33.63        46.26        16.31         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        19.30        23.57        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       14.33        59.18        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 
        1.71         7.36         9.73         8.61        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        6.58         5.72        29.98         4.21         0.79 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.07              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            57.44            122.30 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            11.93             11.57 
[1] "0.1 - 57.4 (11.9)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         0        1       10        8         8        11
  5P GAIN WILD-TYPE       2       12       29       23        28        38
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED           0         18         10          9       10
  5P GAIN WILD-TYPE         3         59         45         28       27
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                12
  STAGE IB                10                29
  STAGE II                 8                23
  STAGE IIA                8                28
  STAGE IIB               11                38
  STAGE III                0                 3
  STAGE IIIA              18                59
  STAGE IIIB              10                45
  STAGE IIIC               9                28
  STAGE IV                10                27
[1] 11  2
[1] TRUE
[1] "dimension of 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     1  23  43  20
  5P GAIN WILD-TYPE  20  64 130  84
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                20
  T2              23                64
  T3              43               130
  T4              20                84
[1] 4 2
[1] TRUE
[1] "dimension of 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   24 26 19 17
  5P GAIN WILD-TYPE 98 81 56 62
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              24                98
  N1              26                81
  N2              19                56
  N3              17                62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  5P GAIN MUTATED    80   6   4
  5P GAIN WILD-TYPE 273  18  14
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              80               273
  M1               6                18
  MX               4                14
[1] 3 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    35  55
  5P GAIN WILD-TYPE 116 189
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     35   55
  5P GAIN WILD-TYPE  116  189
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              35               116
  MALE                55               189
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5P GAIN MUTATED                                       7
  5P GAIN WILD-TYPE                                    58
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                       30
  5P GAIN WILD-TYPE                                                    127
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                                  25
  5P GAIN WILD-TYPE                                                                44
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  5P GAIN MUTATED                                                 15
  5P GAIN WILD-TYPE                                               49
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5P GAIN MUTATED                                                          7
  5P GAIN WILD-TYPE                                                       14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  5P GAIN MUTATED                                                           3
  5P GAIN WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5P GAIN MUTATED                                          1
  5P GAIN WILD-TYPE                                        8
D9V8, multiclass
                                                                   clus
vv                                                                  5P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              25
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  5P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                44
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     2  88
  5P GAIN WILD-TYPE   4 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   88
  5P GAIN WILD-TYPE    4  301
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                2                 4
  YES              88               301
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    74   3   5   5
  5P GAIN WILD-TYPE 244  13  13  20
D9V10, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              74               244
  R1               3                13
  R2               5                13
  RX               5                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"
D9V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5P GAIN MUTATED      18                         1
  5P GAIN WILD-TYPE    70                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           0    54
  5P GAIN WILD-TYPE                                         1   189
D9V12, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                                  18                70
  BLACK OR AFRICAN AMERICAN                               1                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  54               189
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    24   9
  5Q GAIN WILD-TYPE 218 113
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               33               331 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9               113 
$`5Q GAIN MUTATED`
TCGA-BR-7715 TCGA-BR-8284 TCGA-BR-8296 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-A4PD 
       15.42         0.72         1.48         2.96        13.74        20.65 
TCGA-CD-8524 TCGA-CD-A486 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4455 TCGA-CG-4466 
        0.07         6.35         7.99        54.08        12.03        18.97 
TCGA-CG-4472 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-6528 TCGA-D7-8570 TCGA-D7-8576 
       12.00        15.02         4.01        15.22        24.72         6.97 
TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8099 TCGA-HU-8238 
       15.65         0.62         7.79        19.53        17.06         1.51 
TCGA-HU-8249 TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 
       14.17         2.10        12.30         5.56         1.81         5.56 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-VQ-A91X 
       57.44        35.61         8.58 

$`5Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.25         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7716 
       12.82         9.21        24.76        35.24        23.93        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
       12.26         0.49        20.55         0.26        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         1.55         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        0.26        22.19         0.95         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39         0.72         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         0.59        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        0.62        10.68        12.56         1.15         0.66         3.02 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         0.92        13.41        13.51        12.89         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        1.02         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 
       19.07        21.99         9.01         7.07        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
      105.07        12.03        28.96        79.07        65.10        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19         4.14        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       12.33        16.80        19.50        17.19         0.23        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 
        2.96         4.34         7.40         7.13        16.24         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27         8.12         0.39         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        59.54         5.03        13.58         0.56         1.55 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        0.23        18.08        26.47         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.25        10.19         0.26        12.95        19.36        17.69 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IP-7968 TCGA-KB-A6F7 
        1.41         6.44         6.74         6.87         2.53        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT 
       28.90         3.72        19.73         4.31        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.67        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
      116.38        71.38         8.94        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       37.74         5.46        13.25        13.02        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       28.70        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36         9.73        44.25         8.61        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        6.58         5.72        40.08        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.07              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            57.44            122.30 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            12.00             11.57 
[1] "0.1 - 57.4 (12.0)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         0        0        6        4         5         3
  5Q GAIN WILD-TYPE       2       13       33       27        31        46
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           0          5          4          4        4
  5Q GAIN WILD-TYPE         3         72         51         33       33
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                13
  STAGE IB                 6                33
  STAGE II                 4                27
  STAGE IIA                5                31
  STAGE IIB                3                46
  STAGE III                0                 3
  STAGE IIIA               5                72
  STAGE IIIB               4                51
  STAGE IIIC               4                33
  STAGE IV                 4                33
[1] 11  2
[1] TRUE
[1] "dimension of 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     0  11  18   7
  5Q GAIN WILD-TYPE  21  76 155  97
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                21
  T2              11                76
  T3              18               155
  T4               7                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q GAIN MUTATED    13   9   6   7
  5Q GAIN WILD-TYPE 109  98  69  72
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              13               109
  N1               9                98
  N2               6                69
  N3               7                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  5Q GAIN MUTATED    32   2   2
  5Q GAIN WILD-TYPE 321  22  16
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              32               321
  M1               2                22
  MX               2                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    13  23
  5Q GAIN WILD-TYPE 138 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     13   23
  5Q GAIN WILD-TYPE  138  221
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              13               138
  MALE                23               221
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5Q GAIN MUTATED                                       2
  5Q GAIN WILD-TYPE                                    63
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                       11
  5Q GAIN WILD-TYPE                                                    146
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                                  10
  5Q GAIN WILD-TYPE                                                                59
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  5Q GAIN MUTATED                                                  7
  5Q GAIN WILD-TYPE                                               57
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5Q GAIN MUTATED                                                          4
  5Q GAIN WILD-TYPE                                                       17
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  5Q GAIN MUTATED                                                           1
  5Q GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5Q GAIN MUTATED                                          0
  5Q GAIN WILD-TYPE                                        9
D10V8, multiclass
                                                                   clus
vv                                                                  5Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  5Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     1  35
  5Q GAIN WILD-TYPE   5 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1   35
  5Q GAIN WILD-TYPE    5  354
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                1                 5
  YES              35               354
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    31   0   2   1
  5Q GAIN WILD-TYPE 287  16  16  24
D10V10, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              31               287
  R1               0                16
  R2               2                16
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5Q GAIN MUTATED       7                         0
  5Q GAIN WILD-TYPE    81                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    20
  5Q GAIN WILD-TYPE                                         1   223
D10V12, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                                   7                81
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  20               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    37  23
  6P GAIN WILD-TYPE 205  99
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               60               304 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               23                99 
$`6P GAIN MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
        6.61         6.97         0.62         9.21        35.24        15.42 
TCGA-BR-7717 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 
        0.69         1.32        12.95         0.26        14.04        14.79 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 
        0.72         9.21        20.22        11.54        15.68        10.68 
TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48C TCGA-CG-4436 
       20.42         3.25         6.35         0.13         0.13         7.99 
TCGA-CG-4438 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4477 TCGA-D7-6526 
       54.08        12.03        21.99        18.97        30.97        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 
        4.14        15.22        10.55        11.31        12.33         6.97 
TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-8631 TCGA-FP-A4BF 
       14.27         2.96         7.79         0.39         0.56         1.55 
TCGA-HU-8249 TCGA-HU-A4GF TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-8663 TCGA-IN-A6RI 
       14.17        25.81        17.69         9.67         3.39        18.38 
TCGA-IN-A6RO TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-VQ-A8DV 
        1.41         8.61        37.91       115.69         8.94        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
       13.02         2.70        17.85         1.71         8.58         9.73 

$`6P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62        11.70         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       10.13        13.68         7.00        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49         0.82         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 
        0.49        20.55         0.72         0.26        16.31         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.48         7.40         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19         2.96         0.95        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        0.36        19.17         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        5.39         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        0.20         7.53         0.49        15.81        16.44         0.59 
TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        0.62        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.92        13.41        13.51        12.89         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
        0.46        20.65         1.15        13.64        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        2.83        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A489 
        0.10         0.10         0.13         0.13         0.10         0.13 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 
        3.02        27.02        15.95         1.02         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4469 
       14.01        29.98        47.05        19.07         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       12.36        12.66        11.93        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 
       18.54        18.61        17.85         5.95        15.98        12.79 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19         0.23        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       13.71        11.24        11.31        11.44         9.76        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 
        4.34         7.40         7.13         0.62        16.24         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23        21.27         8.12        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX 
       22.29        17.06        59.54         5.03        13.58         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GH 
       12.30        11.84        24.20         3.25        22.75        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        8.88         8.81        27.42        21.21         3.45        18.81 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19        13.08         6.44         6.74         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        5.56         1.81         2.53         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
        3.72        19.73         4.31        11.05         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 
      122.30        40.64       116.38        71.38        57.44        35.61 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 
       16.87         5.79         0.92        37.74         5.46        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       46.26        16.31         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       19.30        23.57        64.57        14.33        59.18        28.70 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Z 
       11.70         8.68        49.25        20.81         7.36        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
        8.61        55.43         4.54         6.58         5.72        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        21.11         4.21         0.79 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.13              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           115.69            122.30 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           10.140            11.885 
[1] "0.1 - 115.7 (10.1)" "0.1 - 122.3 (11.9)"
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         0        2       12        6         4         8
  6P GAIN WILD-TYPE       2       11       27       25        32        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           0         14          9          3        8
  6P GAIN WILD-TYPE         3         63         46         34       29
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                11
  STAGE IB                12                27
  STAGE II                 6                25
  STAGE IIA                4                32
  STAGE IIB                8                41
  STAGE III                0                 3
  STAGE IIIA              14                63
  STAGE IIIB               9                46
  STAGE IIIC               3                34
  STAGE IV                 8                29
[1] 11  2
[1] TRUE
[1] "dimension of 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     3  21  28  14
  6P GAIN WILD-TYPE  18  66 145  90
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               3                18
  T2              21                66
  T3              28               145
  T4              14                90
[1] 4 2
[1] TRUE
[1] "dimension of 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    22  19  15  12
  6P GAIN WILD-TYPE 100  88  60  67
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              22               100
  N1              19                88
  N2              15                60
  N3              12                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  6P GAIN MUTATED    60   4   5
  6P GAIN WILD-TYPE 293  20  13
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              60               293
  M1               4                20
  MX               5                13
[1] 3 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    27  42
  6P GAIN WILD-TYPE 124 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     27   42
  6P GAIN WILD-TYPE  124  202
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              27               124
  MALE                42               202
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6P GAIN MUTATED                                       3
  6P GAIN WILD-TYPE                                    62
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                       30
  6P GAIN WILD-TYPE                                                    127
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                                  19
  6P GAIN WILD-TYPE                                                                50
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  6P GAIN MUTATED                                                 13
  6P GAIN WILD-TYPE                                               51
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6P GAIN MUTATED                                                          1
  6P GAIN WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  6P GAIN MUTATED                                                           1
  6P GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6P GAIN MUTATED                                          2
  6P GAIN WILD-TYPE                                        7
D11V8, multiclass
                                                                   clus
vv                                                                  6P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         30
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  6P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          127
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     3  66
  6P GAIN WILD-TYPE   3 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3   66
  6P GAIN WILD-TYPE    3  323
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                3                 3
  YES              66               323
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    49   3   5   7
  6P GAIN WILD-TYPE 269  13  13  18
D11V10, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              49               269
  R1               3                13
  R2               5                13
  RX               7                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"
D11V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6P GAIN MUTATED      11                         2
  6P GAIN WILD-TYPE    77                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           1    46
  6P GAIN WILD-TYPE                                         0   197
D11V12, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  46               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"

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    27  21
  6Q GAIN WILD-TYPE 215 101
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               316 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               21               101 
$`6Q GAIN MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 
        6.61         6.97         9.21        35.24        15.42         0.69 
TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8484 
        1.32        12.95         0.26        14.04        14.79         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4J1 
        9.21        20.22        11.54        15.68        10.68         0.72 
TCGA-CD-5799 TCGA-CD-A486 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4466 
        3.25         6.35         7.99        54.08        21.99        18.97 
TCGA-CG-4477 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       30.97         4.14        15.22        10.55        11.31        12.33 
TCGA-D7-A4YT TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-A4BF TCGA-HU-A4GT TCGA-HU-A4H6 
       14.27         7.79         0.39         1.55         6.51         9.67 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-RD-A7BT TCGA-RD-A8N6 
        3.45         3.39        18.38         1.41         8.61         8.94 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91U TCGA-VQ-A91X 
       13.25        13.02         2.70        17.85         1.71         8.58 

$`6Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62        11.70         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       10.13        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       23.93        28.01         0.16        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        0.69        12.76        18.71        17.49         0.82         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       12.26         0.49        20.55         0.72         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        1.55         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        3.32         0.36        19.17         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72         5.39         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         0.20         7.53         0.49        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        0.59         0.62        12.56         1.15         0.66         3.02 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         0.92        13.41        13.51        12.89         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        1.02         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       19.07        12.03         9.01         7.07        12.00        22.98 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8570 
       17.85         5.95        17.19        15.98        12.79        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19         0.23         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
       15.65         4.34         7.40         7.13         0.62        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
        6.58        14.47        72.23        21.27         8.12        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.02        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        0.56         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        17.69        12.30         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       27.42        21.21        18.81         5.36         5.19        13.08 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        6.44         6.74         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        28.90         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         4.67        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        5.79         0.92        37.74         5.46        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       16.31         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       23.57        64.57        14.33        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
        8.68        49.25        20.81         7.36         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
        8.61        55.43         4.54         6.58         5.72        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        21.11         4.21         0.79 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.26              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            54.08            122.30 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            9.210            12.015 
[1] "0.3 - 54.1 (9.2)"   "0.1 - 122.3 (12.0)"
[1] "hr=" "1.6"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         0        2       10        5         3         4
  6Q GAIN WILD-TYPE       2       11       29       26        33        45
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           1         13          5          2        8
  6Q GAIN WILD-TYPE         2         64         50         35       29
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                11
  STAGE IB                10                29
  STAGE II                 5                26
  STAGE IIA                3                33
  STAGE IIB                4                45
  STAGE III                1                 2
  STAGE IIIA              13                64
  STAGE IIIB               5                50
  STAGE IIIC               2                35
  STAGE IV                 8                29
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED     3  17  20  13
  6Q GAIN WILD-TYPE  18  70 153  91
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               3                18
  T2              17                70
  T3              20               153
  T4              13                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q GAIN MUTATED    18  16   9  11
  6Q GAIN WILD-TYPE 104  91  66  68
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              18               104
  N1              16                91
  N2               9                66
  N3              11                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  6Q GAIN MUTATED    46   5   4
  6Q GAIN WILD-TYPE 307  19  14
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              46               307
  M1               5                19
  MX               4                14
[1] 3 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    22  33
  6Q GAIN WILD-TYPE 129 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     22   33
  6Q GAIN WILD-TYPE  129  211
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              22               129
  MALE                33               211
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6Q GAIN MUTATED                                       2
  6Q GAIN WILD-TYPE                                    63
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                       26
  6Q GAIN WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                                  16
  6Q GAIN WILD-TYPE                                                                53
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  6Q GAIN MUTATED                                                  8
  6Q GAIN WILD-TYPE                                               56
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6Q GAIN MUTATED                                                          0
  6Q GAIN WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  6Q GAIN MUTATED                                                           1
  6Q GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6Q GAIN MUTATED                                          2
  6Q GAIN WILD-TYPE                                        7
D12V8, multiclass
                                                                   clus
vv                                                                  6Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  6Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 56
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3  52
  6Q GAIN WILD-TYPE   3 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   52
  6Q GAIN WILD-TYPE    3  337
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                3                 3
  YES              52               337
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    39   2   4   6
  6Q GAIN WILD-TYPE 279  14  14  19
D12V10, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              39               279
  R1               2                14
  R2               4                14
  RX               6                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"
D12V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6Q GAIN MUTATED       8                         2
  6Q GAIN WILD-TYPE    80                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           1    36
  6Q GAIN WILD-TYPE                                         0   207
D12V12, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                                   8                80
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  36               207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   103  55
  7P GAIN WILD-TYPE 139  67
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              158               206 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               55                67 
$`7P GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6566 
       11.70         6.97         4.64        10.13         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
       13.84        13.22        21.11         9.21        35.24        15.42 
TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 
        0.69         0.95        12.76        18.71         0.82         0.69 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.72         0.26        12.95         1.55         1.48         7.40 
TCGA-BR-8362 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 
        0.36         0.95         3.32        14.79         0.26         5.39 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
       20.22         1.12        16.44         0.59         0.62        10.68 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 
       22.26         0.92         0.72         0.53        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5801 
       20.65        20.42         1.15        13.64         3.25        13.18 
TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A48A 
        0.10         0.16         0.13         0.10         6.35         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.13         0.07         0.10        20.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4460 TCGA-CG-4469 TCGA-CG-4472 
        7.99         4.01        14.01        21.99         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 
       22.98         1.02        12.03        28.96        79.07        21.07 
TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 
        7.99        12.66        11.93        19.13        18.84        18.54 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 
       17.19         4.14        15.22        15.98        10.55        12.33 
TCGA-D7-8570 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        17.19         0.23         6.97        21.14        20.91 
TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6177 TCGA-F1-6874 
       16.44        15.16         2.96        15.65         6.58        14.47 
TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         0.39        19.53         3.02        22.29        17.06 
TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC 
        0.23        26.47        14.17        24.30        12.30         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 
       22.75        25.81         8.98         0.10        10.19         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD 
       12.95        19.36        17.69        12.30         9.67        27.42 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO 
        3.45        18.81         3.39        18.38         5.19         1.41 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 
        6.44         6.87         5.56        60.56        28.90         4.31 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DV 
        8.61       122.30        57.44         8.94        37.74        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A8PY 
       31.10        21.73        33.63        46.26        17.85        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91U 
       59.18        28.70        11.70         8.68        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        7.36         8.58         4.54        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

$`7P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 
        5.62         6.61         7.43        18.35        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.12        13.68 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        7.00        39.12         0.82        16.14         1.25         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 
       28.01         0.16        18.54        12.43         0.69        17.49 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 TCGA-BR-8291 
        1.32        12.26         0.49        20.55         0.26        16.31 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 
        6.18        19.50         0.26        22.19         2.96        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8382 
        4.31        14.04         0.36        19.17         0.69        15.85 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72         0.72         9.21        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU 
       15.68        12.56         1.15         0.66         3.02        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51        12.89         0.79        14.17        12.82         0.66 
TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 
        0.46        11.57         5.13         2.83        13.15         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.07         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI 
        0.10         0.10         0.13         0.13         0.13         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 
        0.10         3.02         1.02         8.05        54.08        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4477 
       47.05        19.07        12.03         9.01        18.97        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-6519 
       15.02        65.10         4.01        55.04        12.36        20.55 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8572 
       18.61        17.85         5.95        12.79        11.31        16.80 
TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       19.50        14.27         5.92        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       11.24        11.31        11.44         9.76         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C 
        7.13         0.62         7.79        16.24        21.27         8.12 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         1.55        18.08 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        14.27        12.59        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH 
       10.62         0.76         5.59        11.84        24.20        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H8 
       21.37        29.98         6.51         6.25         0.26         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NT 
        8.81        21.21         5.36        13.08         6.74         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW 
        1.81         2.53         3.72        19.73        11.05         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       35.61        16.87         5.79         0.92         5.46        13.02 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PD TCGA-VQ-A8PJ 
       22.36        23.77         7.73        19.07        16.31         2.70 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
        1.87         9.27        23.41        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
       64.57        49.25         9.73        44.25         8.61        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 
        6.58         5.72 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.07              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           122.30            116.38 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           12.165            11.310 
[1] "0.1 - 122.3 (12.2)" "0.1 - 116.4 (11.3)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         2        6       19       14        16        20
  7P GAIN WILD-TYPE       0        7       20       17        20        29
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           2         34         25         19       10
  7P GAIN WILD-TYPE         1         43         30         18       27
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  2                 0
  STAGE IA                 6                 7
  STAGE IB                19                20
  STAGE II                14                17
  STAGE IIA               16                20
  STAGE IIB               20                29
  STAGE III                2                 1
  STAGE IIIA              34                43
  STAGE IIIB              25                30
  STAGE IIIC              19                18
  STAGE IV                10                27
[1] 11  2
[1] TRUE
[1] "dimension of 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   10 38 78 42
  7P GAIN WILD-TYPE 11 49 95 62
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              10                11
  T2              38                49
  T3              78                95
  T4              42                62
[1] 4 2
[1] TRUE
[1] "dimension of 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   57 40 37 34
  7P GAIN WILD-TYPE 65 67 38 45
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              57                65
  N1              40                67
  N2              37                38
  N3              34                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  7P GAIN MUTATED   158   5  11
  7P GAIN WILD-TYPE 195  19   7
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0             158               195
  M1               5                19
  MX              11                 7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    57 117
  7P GAIN WILD-TYPE  94 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     57  117
  7P GAIN WILD-TYPE   94  127
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              57                94
  MALE               117               127
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7P GAIN MUTATED                                      21
  7P GAIN WILD-TYPE                                    44
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                       69
  7P GAIN WILD-TYPE                                                     88
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                                  39
  7P GAIN WILD-TYPE                                                                30
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  7P GAIN MUTATED                                                 28
  7P GAIN WILD-TYPE                                               36
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7P GAIN MUTATED                                                          7
  7P GAIN WILD-TYPE                                                       14
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  7P GAIN MUTATED                                                           4
  7P GAIN WILD-TYPE                                                         4
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7P GAIN MUTATED                                          4
  7P GAIN WILD-TYPE                                        5
D13V8, multiclass
                                                                   clus
vv                                                                  7P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         69
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        4
                                                                   clus
vv                                                                  7P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           88
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     3 171
  7P GAIN WILD-TYPE   3 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3  171
  7P GAIN WILD-TYPE    3  218
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                3                 3
  YES             171               218
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   146   5   6   9
  7P GAIN WILD-TYPE 172  11  12  16
D13V10, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             146               172
  R1               5                11
  R2               6                12
  RX               9                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"
D13V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED      39                         4
  7P GAIN WILD-TYPE    49                         2
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           1   105
  7P GAIN WILD-TYPE                                         0   138
D13V12, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                                  39                49
  BLACK OR AFRICAN AMERICAN                               4                 2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 105               138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    87  49
  7Q GAIN WILD-TYPE 155  73
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              136               228 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               49                73 
$`7Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6565 
       11.70         6.97         4.64        18.35        10.13         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
       32.78        13.84        13.22        21.11         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8284 
       15.42         0.69        12.76        18.71         0.82         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 
        0.26        12.95         1.55         1.48         7.40         0.36 
TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8486 
        0.95         3.32        14.79         0.26         5.39        20.22 
TCGA-BR-8487 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A4IY TCGA-BR-A4J1 
        1.12        16.44         0.59        10.68        12.89         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.53        19.36        13.51        20.65        20.42         1.15 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8536 
        3.25        13.18         0.10         0.16         0.13         0.10 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.13         0.07         0.10        20.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
        7.99         4.01        14.01         7.07        12.00        22.98 
TCGA-CG-5718 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-D7-5578 
        1.02        12.03        28.96        79.07        21.07        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 
       11.93        19.13        18.84        18.54        17.19         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 
       15.22        15.98        24.72        19.50        17.19         6.97 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-F1-6177 
       21.14        20.91        16.44         2.96        15.65         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       14.47        72.23         0.39         3.02        22.29        17.06 
TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GF 
        0.23        26.47        14.17        24.30        12.30        25.81 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        8.98         0.10        10.19         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP 
       17.69        18.81         3.39         5.19         1.41         6.44 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8N5 
        5.56        60.56         4.31         8.61       122.30        57.44 
TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PB 
        8.94        37.74        13.25        31.10        21.73        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       46.26        17.85        14.33        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A925 
        8.68        20.81         1.71         7.36         8.58         4.54 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08        29.98         4.21         0.79 

$`7Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
        5.62         6.61         7.43        30.90         6.18         9.57 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 
        6.61        34.68        15.95        13.12        13.68         7.00 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
       39.12         0.82        16.14         1.25         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       31.20        32.94        12.82        24.76        23.93        28.01 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 
        0.16        18.54        12.43         0.95         0.69        17.49 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8289 
        1.32         0.69        12.26         0.49        20.55         0.26 
TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
       16.31         6.18        19.50         0.26        22.19         2.96 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 
       13.74         4.31        14.04         0.36        19.17         0.69 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8588 TCGA-BR-8589 
       15.85         3.72         0.72         9.21        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.81        15.68         0.62        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        3.02        22.26         0.92        13.41        13.51         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL 
       14.17        12.82         0.66         0.46        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83        13.15         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.07         0.13         0.10         0.10 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI 
        0.13         6.35         0.13         0.13         0.13         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4443 
        0.10         3.02         1.02         8.05        54.08        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 
       47.05        19.07        12.03        21.99         9.01        18.97 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 
      105.07        15.02        65.10         4.01        55.04         7.99 
TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 
       12.36        20.55        18.61        17.85         5.95        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-A4YT 
       10.55        11.31        12.33        16.80         0.23        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.31        11.44         9.76         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
        0.62         7.79        16.24        21.27         8.12        19.53 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         1.55        18.08 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        14.27        12.59        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       10.62         0.76         5.59        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GU 
       22.75        11.77        21.37        29.98         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        0.26        12.30         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR 
       21.21         3.45        18.38         5.36        13.08         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A93H TCGA-MX-A5UG 
        6.87         5.56         1.81         2.53        28.90         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 
       19.73        11.05         4.67        16.67        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
      115.69       116.38        71.38        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
        0.92         5.46        13.02        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       19.07        16.31         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91K TCGA-VQ-A91Y 
       15.65        19.30        23.57        64.57        49.25         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6J 
       44.25         8.61        55.43         6.58         5.72        21.11 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.07              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           122.30            116.38 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           12.710            11.145 
[1] "0.1 - 122.3 (12.7)" "0.1 - 116.4 (11.1)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         2        5       16       13        14        15
  7Q GAIN WILD-TYPE       0        8       23       18        22        34
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           1         28         22         17        9
  7Q GAIN WILD-TYPE         2         49         33         20       28
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  2                 0
  STAGE IA                 5                 8
  STAGE IB                16                23
  STAGE II                13                18
  STAGE IIA               14                22
  STAGE IIB               15                34
  STAGE III                1                 2
  STAGE IIIA              28                49
  STAGE IIIB              22                33
  STAGE IIIC              17                20
  STAGE IV                 9                28
[1] 11  2
[1] TRUE
[1] "dimension of 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     8  35  65  36
  7Q GAIN WILD-TYPE  13  52 108  68
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               8                13
  T2              35                52
  T3              65               108
  T4              36                68
[1] 4 2
[1] TRUE
[1] "dimension of 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   51 31 31 31
  7Q GAIN WILD-TYPE 71 76 44 48
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              51                71
  N1              31                76
  N2              31                44
  N3              31                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  7Q GAIN MUTATED   136   3  12
  7Q GAIN WILD-TYPE 217  21   6
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0             136               217
  M1               3                21
  MX              12                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    50 101
  7Q GAIN WILD-TYPE 101 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     50  101
  7Q GAIN WILD-TYPE  101  143
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              50               101
  MALE               101               143
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7Q GAIN MUTATED                                      17
  7Q GAIN WILD-TYPE                                    48
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                       61
  7Q GAIN WILD-TYPE                                                     96
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                                  35
  7Q GAIN WILD-TYPE                                                                34
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  7Q GAIN MUTATED                                                 23
  7Q GAIN WILD-TYPE                                               41
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7Q GAIN MUTATED                                                          6
  7Q GAIN WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  7Q GAIN MUTATED                                                           3
  7Q GAIN WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7Q GAIN MUTATED                                          4
  7Q GAIN WILD-TYPE                                        5
D14V8, multiclass
                                                                   clus
vv                                                                  7Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          17
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         61
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              35
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        4
                                                                   clus
vv                                                                  7Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            48
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                34
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2 149
  7Q GAIN WILD-TYPE   4 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  149
  7Q GAIN WILD-TYPE    4  240
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                2                 4
  YES             149               240
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   126   4   5  11
  7Q GAIN WILD-TYPE 192  12  13  14
D14V10, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             126               192
  R1               4                12
  R2               5                13
  RX              11                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"
D14V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED      31                         3
  7Q GAIN WILD-TYPE    57                         3
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           1    93
  7Q GAIN WILD-TYPE                                         0   150
D14V12, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                                  31                57
  BLACK OR AFRICAN AMERICAN                               3                 3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  93               150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   105  44
  8P GAIN WILD-TYPE 137  78
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              149               215 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               44                78 
$`8P GAIN MUTATED`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-6452 
        5.62         6.61         6.97         4.64        30.90        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6707 TCGA-BR-6802 
       15.95        13.12        13.68         0.62        16.14        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7957 
       31.20        32.94        35.24        23.93        15.42         0.69 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8297 TCGA-BR-8368 
        1.32        12.26         0.49         0.72         7.40         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 
       14.04         3.32        19.17         0.26        15.85         5.39 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-A452 
        9.21        20.22         2.14        13.45         7.53         0.66 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 
       22.26         0.92        13.41        12.82        19.36         0.46 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8530 TCGA-CD-8536 
       20.42        11.57        13.15         0.07         0.16         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 
        6.35         0.13         0.07         0.10        20.02        15.95 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 
       14.01        47.05        12.03        21.99        18.97         7.07 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
       12.00         1.02         0.99        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       65.10        21.07        12.66        11.93        19.13        18.84 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85        17.19        12.79        10.55        11.31        12.33 
TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EV 
        6.97        20.91         5.92        15.16        14.76        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A748 TCGA-EQ-5647 TCGA-EQ-A4SO 
       11.31        11.44         2.96         4.34         0.62        16.24 
TCGA-F1-A448 TCGA-FP-7829 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       21.27        19.53         1.55         0.23        18.08        26.47 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 
       14.27        12.59        11.41        24.30        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        22.75        25.81        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.10         0.26         2.10        19.36        17.69        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RS 
        8.88         8.81         3.45         3.39         5.19         6.87 
TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7C1 
        5.56        60.56        28.90        19.73         4.31        16.67 
TCGA-RD-A8N1 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
      115.69        16.87         5.79         0.92        37.74         5.46 
TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       22.36        19.07        33.63        16.31         2.70         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91E 
       23.41        19.30        23.57        64.57        28.70         8.68 
TCGA-VQ-A91W TCGA-VQ-A927 TCGA-VQ-A928 TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        7.36         6.58         5.72         4.21         0.79 

$`8P GAIN WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       11.70         7.43        18.35         6.18         9.57         6.61 
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       10.13         7.00        39.12         0.82        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7197 
       13.22         1.25         8.98        21.11        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       24.76        28.01         0.69         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        0.95        12.76        18.71        17.49         0.82         0.69 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         0.26        12.95         0.26        16.31         1.55 
TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        1.48         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8371 TCGA-BR-8373 TCGA-BR-8380 
        2.96         0.95        13.74         0.36        14.79         0.69 
TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8592 
        3.72         0.72         1.12        12.79        15.81         0.20 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         0.59        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IV 
        0.62        10.68        12.56         1.15         3.02        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 
       12.89         0.79         0.72        14.17         0.53         0.66 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 
       13.51        20.65         1.15        13.64         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        3.25        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.10         0.13         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.13         0.10         0.10 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4475 TCGA-CG-4477 
        4.01        29.98        19.07         9.01        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
        6.97         1.02         0.99         6.02       105.07        12.03 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 
        4.01        55.04         7.99        12.36        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8570 
       18.61         5.95         4.14        15.22        15.98        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT 
       16.80        19.50        17.19         0.23        21.14        14.27 
TCGA-D7-A4YU TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A74A 
       16.44        13.78        13.71         9.76        15.65         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C 
        7.13         7.79         6.58        14.47        72.23         8.12 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.39         3.02        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 
       13.58         0.56         1.51         5.92        14.17        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GT 
       10.62         0.76         5.59        11.77        21.37         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
        6.25        10.19        12.95         9.67        27.42        21.21 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.81        18.38         5.36        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-RD-A7BS 
        6.74         1.81         2.53         5.56         3.72        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         4.67       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       71.38        57.44         8.94        35.61        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PK 
       31.10        21.73        23.77         7.73        46.26        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K 
        1.87        15.65        14.33        59.18        11.70        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       20.81         1.71         8.58         9.73        44.25         8.61 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
       55.43         4.54        40.08        29.98        21.11 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.07              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           115.69            122.30 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            12.30              9.76 
[1] "0.1 - 115.7 (12.3)" "0.1 - 122.3 (9.8)" 
[1] "hr=" "1.3"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         1        7       18       12        16        24
  8P GAIN WILD-TYPE       1        6       21       19        20        25
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           1         32         17         16       12
  8P GAIN WILD-TYPE         2         45         38         21       25
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 7                 6
  STAGE IB                18                21
  STAGE II                12                19
  STAGE IIA               16                20
  STAGE IIB               24                25
  STAGE III                1                 2
  STAGE IIIA              32                45
  STAGE IIIB              17                38
  STAGE IIIC              16                21
  STAGE IV                12                25
[1] 11  2
[1] TRUE
[1] "dimension of 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    11  42  64  42
  8P GAIN WILD-TYPE  10  45 109  62
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              11                10
  T2              42                45
  T3              64               109
  T4              42                62
[1] 4 2
[1] TRUE
[1] "dimension of 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   53 41 29 34
  8P GAIN WILD-TYPE 69 66 46 45
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              53                69
  N1              41                66
  N2              29                46
  N3              34                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  8P GAIN MUTATED   151   8   7
  8P GAIN WILD-TYPE 202  16  11
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0             151               202
  M1               8                16
  MX               7                11
[1] 3 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    72  94
  8P GAIN WILD-TYPE  79 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     72   94
  8P GAIN WILD-TYPE   79  150
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              72                79
  MALE                94               150
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8P GAIN MUTATED                                      28
  8P GAIN WILD-TYPE                                    37
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                       61
  8P GAIN WILD-TYPE                                                     96
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                                  26
  8P GAIN WILD-TYPE                                                                43
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  8P GAIN MUTATED                                                 27
  8P GAIN WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8P GAIN MUTATED                                                         13
  8P GAIN WILD-TYPE                                                        8
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  8P GAIN MUTATED                                                           6
  8P GAIN WILD-TYPE                                                         2
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8P GAIN MUTATED                                          4
  8P GAIN WILD-TYPE                                        5
D15V8, multiclass
                                                                   clus
vv                                                                  8P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          28
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         61
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              26
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        4
                                                                   clus
vv                                                                  8P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            37
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           96
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                43
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     4 162
  8P GAIN WILD-TYPE   2 227
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4  162
  8P GAIN WILD-TYPE    2  227
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                4                 2
  YES             162               227
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED   129  10   5  15
  8P GAIN WILD-TYPE 189   6  13  10
D15V10, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0             129               189
  R1              10                 6
  R2               5                13
  RX              15                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"
D15V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8P GAIN MUTATED      33                         1
  8P GAIN WILD-TYPE    55                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           0   105
  8P GAIN WILD-TYPE                                         1   138
D15V12, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                                  33                55
  BLACK OR AFRICAN AMERICAN                               1                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 105               138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   131  63
  8Q GAIN WILD-TYPE 111  59
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              194               170 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               63                59 
$`8Q GAIN MUTATED`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-6452 
        5.62         6.61         6.97         4.64        30.90        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6707 
       15.95        13.12        10.13        13.68         0.62        16.14 
TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7197 TCGA-BR-7704 
        1.25        30.90        31.20        32.94         9.21        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8060 
       23.93        15.42        28.01         0.69        12.76         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8296 TCGA-BR-8297 
        0.69        12.26         0.49         0.72         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8362 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        6.18         0.36        13.74         4.31        14.04         3.32 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
       19.17         0.26        15.85         5.39         9.21        20.22 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8676 TCGA-BR-8682 TCGA-BR-8687 
       12.79         2.14        13.45         7.53        16.44         0.62 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4J1 
        1.15         0.66        22.26         0.92        13.41         0.72 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-CD-5800 TCGA-CD-5803 
       12.82        19.36         0.46        11.57        13.15         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.07         0.07         0.16         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4305 
        6.35         0.13         0.07         0.10        20.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        7.99         8.05        54.08        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-5718 
       12.03        21.99        18.97         7.07        12.00         1.02 
TCGA-CG-5722 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 
       55.04        21.07        12.66        11.93        19.13        18.84 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85         5.95        17.19        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YU 
       10.55        11.31        12.33         6.97        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
        5.92        15.16        14.76        11.24        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        2.96        15.65         4.34         0.62         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8631 
        6.58        72.23        21.27         0.39        19.53         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        1.55         0.23        26.47         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       11.41         0.76        24.30        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        22.75        25.81        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         6.25         0.26         2.10        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 
       12.30         8.88         8.81        27.42         3.45         3.39 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
        5.19         1.41         6.44         6.74         6.87         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7C1 
       60.56        28.90        19.73         4.31        11.05        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
      115.69        71.38        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8P2 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
        5.46        13.25        22.36        19.07        33.63        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        2.70         9.27        23.41        19.30        23.57        64.57 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91W TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
       28.70         8.68         7.36         6.58         5.72        40.08 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

$`8Q GAIN WILD-TYPE`
TCGA-B7-5818 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       11.70         7.43        18.35         6.18         9.57         6.61 
TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
        7.00        39.12         0.82        32.78        13.84        13.22 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7717 TCGA-BR-7722 
        8.98        21.11        12.82        24.76         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       18.54        12.43         0.95        18.71        17.49         0.82 
TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
       20.55         0.26        12.95         0.26        16.31         1.55 
TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8371 
       19.50         0.26        22.19         2.96         0.95         0.36 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8589 
       14.79         0.69         3.72         0.72         1.12        15.81 
TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 
        0.20         0.49        11.54        15.81         0.59        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       10.68        12.56         3.02        13.51        12.89         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE 
       14.17         0.53         0.66        13.51        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
        1.15        13.64         5.13         2.83         3.25        13.18 
TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
        0.30         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
        0.10         0.13         0.13         0.13         0.10         0.10 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4465 
        3.02        27.02         1.02         4.01        19.07         9.01 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6521 
      105.07        12.03         7.99        12.36        20.55        18.54 
TCGA-D7-6522 TCGA-D7-6527 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       18.61         4.14        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EZ 
        0.23        21.14        14.27        13.78        13.71         9.76 
TCGA-D7-A74A TCGA-D7-A74B TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 
        7.40         7.13        14.47         8.12         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HU-8238 
       17.06        59.54         5.03        13.58        18.08         1.51 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4GH TCGA-HU-A4GJ 
       14.17        12.10        10.62         5.59        11.77        21.37 
TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI 
       10.19        12.95         9.67        21.21        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG 
        5.36        13.08         1.81         2.53         5.56         3.72 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         4.67       122.30        37.91        40.64       116.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       57.44         8.94        35.61        13.02        31.10        21.73 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PQ 
       23.77         7.73        46.26        17.85         1.87        15.65 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       14.33        59.18        11.70        49.25        20.81         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 
        8.58         9.73        44.25         8.61        55.43         4.54 
TCGA-VQ-AA6B TCGA-VQ-AA6J 
       29.98        21.11 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           115.69            122.30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           11.505            11.700 
[1] "0.1 - 115.7 (11.5)" "0.1 - 122.3 (11.7)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         2       11       22       15        18        31
  8Q GAIN WILD-TYPE       0        2       17       16        18        18
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           1         43         23         21       15
  8Q GAIN WILD-TYPE         2         34         32         16       22
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  2                 0
  STAGE IA                11                 2
  STAGE IB                22                17
  STAGE II                15                16
  STAGE IIA               18                18
  STAGE IIB               31                18
  STAGE III                1                 2
  STAGE IIIA              43                34
  STAGE IIIB              23                32
  STAGE IIIC              21                16
  STAGE IV                15                22
[1] 11  2
[1] TRUE
[1] "dimension of 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   16 52 86 52
  8Q GAIN WILD-TYPE  5 35 87 52
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              16                 5
  T2              52                35
  T3              86                87
  T4              52                52
[1] 4 2
[1] TRUE
[1] "dimension of 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   68 58 36 42
  8Q GAIN WILD-TYPE 54 49 39 37
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              68                54
  N1              58                49
  N2              36                39
  N3              42                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  8Q GAIN MUTATED   193   9  12
  8Q GAIN WILD-TYPE 160  15   6
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0             193               160
  M1               9                15
  MX              12                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    87 127
  8Q GAIN WILD-TYPE  64 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     87  127
  8Q GAIN WILD-TYPE   64  117
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              87                64
  MALE               127               117
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8Q GAIN MUTATED                                      32
  8Q GAIN WILD-TYPE                                    33
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                       82
  8Q GAIN WILD-TYPE                                                     75
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                                  39
  8Q GAIN WILD-TYPE                                                                30
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  8Q GAIN MUTATED                                                 36
  8Q GAIN WILD-TYPE                                               28
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8Q GAIN MUTATED                                                         14
  8Q GAIN WILD-TYPE                                                        7
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  8Q GAIN MUTATED                                                           6
  8Q GAIN WILD-TYPE                                                         2
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8Q GAIN MUTATED                                          4
  8Q GAIN WILD-TYPE                                        5
D16V8, multiclass
                                                                   clus
vv                                                                  8Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          32
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         82
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                       14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        4
                                                                   clus
vv                                                                  8Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            33
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           75
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     5 209
  8Q GAIN WILD-TYPE   1 180
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5  209
  8Q GAIN WILD-TYPE    1  180
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                5                 1
  YES             209               180
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   171  12   6  17
  8Q GAIN WILD-TYPE 147   4  12   8
D16V10, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             171               147
  R1              12                 4
  R2               6                12
  RX              17                 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"
D16V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8Q GAIN MUTATED      45                         4
  8Q GAIN WILD-TYPE    43                         2
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           0   132
  8Q GAIN WILD-TYPE                                         1   111
D16V12, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                                  45                43
  BLACK OR AFRICAN AMERICAN                               4                 2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 132               111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    35  15
  9P GAIN WILD-TYPE 207 107
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               50               314 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               15               107 
$`9P GAIN MUTATED`
TCGA-BR-6456 TCGA-BR-6707 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7959 
       10.13        16.14        23.93        15.42         0.69        18.71 
TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-A4J4 
        0.49         0.26         1.55        12.79        16.44         0.53 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8535 TCGA-CD-A4MH 
        0.46        20.42         2.83        13.18         0.13         0.10 
TCGA-CG-4436 TCGA-CG-4444 TCGA-CG-4477 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 
        7.99        47.05        30.97        15.22        10.55        12.33 
TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-A8CX TCGA-HF-A5NB 
       14.76        11.44         0.62        21.27         0.23        18.08 
TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H0 
       14.17         0.76        12.30        22.75         8.98         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-8663 TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-RD-A8MV 
       12.95        12.30         3.39         6.44        60.56       122.30 
TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PP TCGA-VQ-A91Z 
      115.69        35.61         5.46        46.26        23.41        44.25 
TCGA-VQ-A922 TCGA-VQ-A928 
        8.61         5.72 

$`9P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.12        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 
        0.62        32.78        13.84        13.22         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       24.76        35.24        28.01         0.16        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69        12.76        17.49         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69        12.26        20.55         0.72         0.26        12.95 
TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
       16.31         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
       14.04         3.32         0.36        19.17        14.79         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       20.22         1.12        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        11.54        15.81         0.59        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        0.62        10.68        12.56         1.15         0.66         3.02 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         0.92        13.41        13.51        12.89         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17        12.82         0.66        19.36        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 
       20.65         1.15        13.64        11.57         5.13         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.13         0.07         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
       14.01        29.98        19.07        12.03        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        22.98         6.97         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8570 
       17.19         4.14        15.98        12.79        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19         0.23         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.24        11.31         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 
        4.34         7.40         7.13         7.79        16.24         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        72.23         8.12         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        1.55        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       11.41        12.10        10.62        24.30         5.59        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
        0.10         6.51         6.25        10.19         0.26        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       17.69         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        1.41         6.74         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
        5.56        28.90         3.72        19.73         4.31        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
        8.61         4.67        16.67        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       37.74        13.25        13.02        31.10        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ 
       23.77         7.73        19.07        33.63        16.31         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
       17.85         1.87         9.27        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       49.25        20.81         1.71         7.36         8.58         9.73 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
       55.43         4.54         6.58        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.10              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           122.30            116.38 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           12.315            11.475 
[1] "0.1 - 122.3 (12.3)" "0.1 - 116.4 (11.5)"
[1] "hr=" "1.3"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         1        2        8        3         5         7
  9P GAIN WILD-TYPE       1       11       31       28        31        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           0          9          6          5        6
  9P GAIN WILD-TYPE         3         68         49         32       31
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 2                11
  STAGE IB                 8                31
  STAGE II                 3                28
  STAGE IIA                5                31
  STAGE IIB                7                42
  STAGE III                0                 3
  STAGE IIIA               9                68
  STAGE IIIB               6                49
  STAGE IIIC               5                32
  STAGE IV                 6                31
[1] 11  2
[1] TRUE
[1] "dimension of 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     6  14  19  14
  9P GAIN WILD-TYPE  15  73 154  90
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               6                15
  T2              14                73
  T3              19               154
  T4              14                90
[1] 4 2
[1] TRUE
[1] "dimension of 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    18  15   8  12
  9P GAIN WILD-TYPE 104  92  67  67
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              18               104
  N1              15                92
  N2               8                67
  N3              12                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  9P GAIN MUTATED    51   2   1
  9P GAIN WILD-TYPE 302  22  17
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0              51               302
  M1               2                22
  MX               1                17
[1] 3 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    20  34
  9P GAIN WILD-TYPE 131 210
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     20   34
  9P GAIN WILD-TYPE  131  210
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              20               131
  MALE                34               210
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9P GAIN MUTATED                                       6
  9P GAIN WILD-TYPE                                    59
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                       18
  9P GAIN WILD-TYPE                                                    139
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                                   6
  9P GAIN WILD-TYPE                                                                63
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  9P GAIN MUTATED                                                 11
  9P GAIN WILD-TYPE                                               53
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9P GAIN MUTATED                                                          8
  9P GAIN WILD-TYPE                                                       13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  9P GAIN MUTATED                                                           3
  9P GAIN WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9P GAIN MUTATED                                          2
  9P GAIN WILD-TYPE                                        7
D17V8, multiclass
                                                                   clus
vv                                                                  9P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  9P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  52
  9P GAIN WILD-TYPE   4 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   52
  9P GAIN WILD-TYPE    4  337
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                2                 4
  YES              52               337
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    46   3   1   2
  9P GAIN WILD-TYPE 272  13  17  23
D17V10, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              46               272
  R1               3                13
  R2               1                17
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9P GAIN MUTATED      15                         0
  9P GAIN WILD-TYPE    73                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           0    30
  9P GAIN WILD-TYPE                                         1   213
D17V12, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                                  15                73
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  30               213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    43  19
  9Q GAIN WILD-TYPE 199 103
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               62               302 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               19               103 
$`9Q GAIN MUTATED`
TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6707 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       18.35        10.13        16.14        35.24        23.93        15.42 
TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 
        0.69        18.71         0.49         0.26         1.55         6.18 
TCGA-BR-8588 TCGA-BR-8682 TCGA-BR-A4CQ TCGA-BR-A4J4 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.79        16.44        22.26         0.53         0.46        20.65 
TCGA-BR-A4PE TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-8535 TCGA-CG-4436 TCGA-CG-4444 
       20.42         2.83        13.18         0.13         7.99        47.05 
TCGA-CG-4477 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-A4YT 
       30.97        12.66        17.19        15.22        10.55        14.27 
TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-F1-A448 TCGA-FP-7735 
       14.76        11.44        15.65         0.62        21.27         0.39 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4G6 
        0.23        18.08         1.51        14.17         0.76        12.30 
TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4H5 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RO 
       22.75         8.98        12.30         3.45         3.39         1.41 
TCGA-IN-A6RP TCGA-KB-A6F7 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-VQ-A8DT 
        6.44        60.56       122.30       115.69        35.61        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A91X TCGA-VQ-A91Z 
        5.46        46.26        23.41        23.57         8.58        44.25 
TCGA-VQ-A922 TCGA-VQ-A928 
        8.61         5.72 

$`9Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.12        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       32.78        13.84        13.22         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       12.76        17.49         0.82         1.32         0.69        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 
       20.55         0.72         0.26        12.95        16.31         1.48 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        7.40        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 
        5.39         0.72         9.21        20.22         1.12        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        1.15         0.66         3.02         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         0.79         0.72        14.17        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM 
       19.36        13.51         1.15        13.64        11.57         5.13 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
        3.25        13.15         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 
       20.02         3.02        27.02        15.95         1.02         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         9.01        18.97         7.07        12.00        22.98 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 
        4.01        55.04        21.07         7.99        12.36        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
        5.95         4.14        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19         0.23         6.97 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        15.16        13.78 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 
       13.71        11.24        11.31         9.76         2.96         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.40         7.13         7.79        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       72.23         8.12        19.53         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 
       59.54         5.03        13.58         0.56         1.55        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        5.92        14.27        12.59        11.41        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
       24.30         5.59        11.84        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       11.77        21.37        29.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        17.69 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        9.67         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38         5.36         5.19        13.08         6.74         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG 
        5.56         1.81         2.53         5.56        28.90         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       19.73         4.31        11.05         8.61         4.67        16.67 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       37.91        40.64       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
       16.87         5.79         0.92        13.25        13.02        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ 
       16.31         2.70        17.85         1.87         9.27        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       19.30        64.57        14.33        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
        8.68        49.25        20.81         1.71         7.36         9.73 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
       55.43         4.54         6.58        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.13              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           122.30            116.38 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           12.985            11.310 
[1] "0.1 - 122.3 (13.0)" "0.1 - 116.4 (11.3)"
[1] "hr=" "1.3"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         1        3        9        4         5         8
  9Q GAIN WILD-TYPE       1       10       30       27        31        41
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           1         15          8          4        6
  9Q GAIN WILD-TYPE         2         62         47         33       31
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 3                10
  STAGE IB                 9                30
  STAGE II                 4                27
  STAGE IIA                5                31
  STAGE IIB                8                41
  STAGE III                1                 2
  STAGE IIIA              15                62
  STAGE IIIB               8                47
  STAGE IIIC               4                33
  STAGE IV                 6                31
[1] 11  2
[1] TRUE
[1] "dimension of 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     7  16  26  16
  9Q GAIN WILD-TYPE  14  71 147  88
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               7                14
  T2              16                71
  T3              26               147
  T4              16                88
[1] 4 2
[1] TRUE
[1] "dimension of 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    22  19  12  13
  9Q GAIN WILD-TYPE 100  88  63  66
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              22               100
  N1              19                88
  N2              12                63
  N3              13                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  9Q GAIN MUTATED    62   3   2
  9Q GAIN WILD-TYPE 291  21  16
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0              62               291
  M1               3                21
  MX               2                16
[1] 3 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    22  45
  9Q GAIN WILD-TYPE 129 199
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     22   45
  9Q GAIN WILD-TYPE  129  199
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              22               129
  MALE                45               199
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9Q GAIN MUTATED                                       6
  9Q GAIN WILD-TYPE                                    59
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                       23
  9Q GAIN WILD-TYPE                                                    134
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                                  10
  9Q GAIN WILD-TYPE                                                                59
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  9Q GAIN MUTATED                                                 15
  9Q GAIN WILD-TYPE                                               49
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9Q GAIN MUTATED                                                          8
  9Q GAIN WILD-TYPE                                                       13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  9Q GAIN MUTATED                                                           3
  9Q GAIN WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9Q GAIN MUTATED                                          2
  9Q GAIN WILD-TYPE                                        7
D18V8, multiclass
                                                                   clus
vv                                                                  9Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  9Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  65
  9Q GAIN WILD-TYPE   4 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   65
  9Q GAIN WILD-TYPE    4  324
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                2                 4
  YES              65               324
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    58   3   1   3
  9Q GAIN WILD-TYPE 260  13  17  22
D18V10, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              58               260
  R1               3                13
  R2               1                17
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9Q GAIN MUTATED      15                         1
  9Q GAIN WILD-TYPE    73                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           0    41
  9Q GAIN WILD-TYPE                                         1   202
D18V12, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                                  15                73
  BLACK OR AFRICAN AMERICAN                               1                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  41               202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    55  31
  10P GAIN WILD-TYPE 187  91
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                86                278 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                31                 91 
$`10P GAIN MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6565 TCGA-BR-6801 TCGA-BR-7197 
        6.61        10.13        13.68         0.62        21.11         9.21 
TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8077 
       35.24        15.42        28.01         0.69        18.54         0.69 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.49        12.95         0.26         1.55         1.48         7.40 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A4J1 TCGA-BR-A4J7 
        5.39         9.21        16.44         0.59         0.72        19.36 
TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8524 
       13.51        20.65         1.15        13.64        13.18         0.07 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4300 
        0.07         0.16         0.13         0.13         0.13        20.02 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5730 
        4.01        47.05        21.99        12.00        30.97         4.01 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-8578 
       19.13        20.55        18.84        17.19        10.55        21.14 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 
       16.44        11.31        15.65         7.40         0.62        72.23 
TCGA-FP-7735 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 
        0.39         1.51         5.92        11.41         0.76        12.30 
TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H2 
       24.20        22.75        25.81        11.77         6.25        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-KB-A93H 
       17.69         9.67        27.42         3.45         3.39        28.90 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-VQ-A8DU TCGA-VQ-A8E3 
       11.05         8.61        16.67       122.30         5.46        21.73 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91U 
        7.73        46.26        64.57        14.33         8.68         1.71 
TCGA-VQ-A925 TCGA-VQ-AA6J 
        4.54        21.11 

$`10P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.12         7.00        39.12         0.82        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       13.22        16.14         1.25         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7851 
       32.94        12.82        24.76        23.93         0.16        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        0.95         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
        1.32        12.26        20.55         0.72         0.26        16.31 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        0.72        20.22         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         0.62        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        3.02        22.26         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J9 
        0.79        14.17         0.53        12.82         0.66         0.46 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.42        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         6.35 
TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        0.13         0.07         0.10         0.10         0.10         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
        7.07        22.98         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        6.02         0.99       105.07        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       12.66        11.93        18.54        18.61        17.85         5.95 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
        4.14        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19         0.23         6.97 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 
       13.71        11.24        11.44         9.76         2.96         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        7.13         7.79        16.24         6.58        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        8.12        19.53         3.02        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         1.55         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 
       26.47        14.27        12.59        14.17        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.30         5.59        11.84         3.25        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       19.36        12.30         8.88         8.81        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.38         5.36         5.19        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
        6.74         6.87         5.56         1.81         2.53         5.56 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BW TCGA-RD-A8MW 
       60.56         3.72        19.73         4.31         4.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       35.61        16.87         5.79         0.92        37.74        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       13.02        31.10        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        19.30        23.57        59.18        28.70        11.70 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       49.25        20.81         7.36         8.58         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B 
        8.61        55.43         6.58         5.72        40.08        29.98 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.07               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            122.30             116.38 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             11.36              11.70 
[1] "0.1 - 122.3 (11.4)" "0.1 - 116.4 (11.7)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         0        6        6        5         8        15
  10P GAIN WILD-TYPE       2        7       33       26        28        34
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           1         20         14          6        9
  10P GAIN WILD-TYPE         2         57         41         31       28
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  6                  7
  STAGE IB                  6                 33
  STAGE II                  5                 26
  STAGE IIA                 8                 28
  STAGE IIB                15                 34
  STAGE III                 1                  2
  STAGE IIIA               20                 57
  STAGE IIIB               14                 41
  STAGE IIIC                6                 31
  STAGE IV                  9                 28
[1] 11  2
[1] TRUE
[1] "dimension of 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     5  15  47  24
  10P GAIN WILD-TYPE  16  72 126  80
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                5                 16
  T2               15                 72
  T3               47                126
  T4               24                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  10P GAIN MUTATED   31 22 21 16
  10P GAIN WILD-TYPE 91 85 54 63
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               31                 91
  N1               22                 85
  N2               21                 54
  N3               16                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  10P GAIN MUTATED    83   6   3
  10P GAIN WILD-TYPE 270  18  15
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0               83                270
  M1                6                 18
  MX                3                 15
[1] 3 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    35  57
  10P GAIN WILD-TYPE 116 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     35   57
  10P GAIN WILD-TYPE  116  187
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               35                116
  MALE                 57                187
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10P GAIN MUTATED                                      13
  10P GAIN WILD-TYPE                                    52
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                       33
  10P GAIN WILD-TYPE                                                    124
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                                  18
  10P GAIN WILD-TYPE                                                                51
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  10P GAIN MUTATED                                                 22
  10P GAIN WILD-TYPE                                               42
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10P GAIN MUTATED                                                          3
  10P GAIN WILD-TYPE                                                       18
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  10P GAIN MUTATED                                                           1
  10P GAIN WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10P GAIN MUTATED                                          1
  10P GAIN WILD-TYPE                                        8
D19V8, multiclass
                                                                   clus
vv                                                                  10P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               18
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                22
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  10P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 51
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2  90
  10P GAIN WILD-TYPE   4 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   90
  10P GAIN WILD-TYPE    4  299
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                  4
  YES               90                299
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    76   1   6   5
  10P GAIN WILD-TYPE 242  15  12  20
D19V10, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               76                242
  R1                1                 15
  R2                6                 12
  RX                5                 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"
D19V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10P GAIN MUTATED      27                         3
  10P GAIN WILD-TYPE    61                         3
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           1    51
  10P GAIN WILD-TYPE                                         0   192
D19V12, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                                   27                 61
  BLACK OR AFRICAN AMERICAN                                3                  3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   51                192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    38  24
  10Q GAIN WILD-TYPE 204  98
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                62                302 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                24                 98 
$`10Q GAIN MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
        6.61        10.13         0.82         9.21        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
       28.01        18.54         0.69        12.95         0.26         1.48 
TCGA-BR-8297 TCGA-BR-8682 TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF 
        7.40        16.44         0.72        19.36        20.65         1.15 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8533 TCGA-CG-4300 
       13.18         0.07         0.07         0.16         0.13        20.02 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4477 TCGA-D7-6519 TCGA-D7-6520 
       47.05        21.99        12.00        30.97        20.55        18.84 
TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV 
       17.19        10.55         0.23        21.14        16.44        11.24 
TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-FP-7735 TCGA-HU-8238 
       11.31         7.40         0.62        72.23         0.39         1.51 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4H4 
       11.41         0.76        12.30        24.20        22.75        17.69 
TCGA-HU-A4H6 TCGA-IN-7808 TCGA-IN-8663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A8MV 
        9.67         3.45         3.39        11.05         8.61       122.30 
TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q 
       21.73        46.26        64.57        14.33         8.68        20.81 
TCGA-VQ-A925 TCGA-VQ-A928 
        4.54         5.72 

$`10Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       13.12        13.68         7.00        39.12         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.69         0.16        12.43         0.95         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49         0.82         1.32        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8360 
       20.55         0.72         0.26        16.31         1.55         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       14.79         0.69         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.72         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
        1.15         0.66         3.02        22.26         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51        12.89         0.79        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL 
        0.66        13.51         0.46        20.42        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.13         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        0.13         0.07         0.10         0.10         0.10         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 
        4.01        14.01        29.98        19.07        12.03         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       18.97         7.07        22.98         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 
        7.99        12.36        12.66        11.93        19.13        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85         5.95         4.14        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       17.19         6.97        20.91        14.27         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.78        14.76        13.71        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 
       15.65         4.34         7.13         7.79        16.24         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27         8.12        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         1.55 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
        0.23        18.08        26.47         5.92        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       14.17        12.10        10.62        24.30         5.59        11.84 
TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        19.36        12.30         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       21.21        18.81        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        1.41         6.44         6.74         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.31         4.67        16.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        37.74         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       31.10        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        19.30        23.57        59.18        28.70        11.70 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       49.25         1.71         7.36         8.58         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        8.61        55.43         6.58        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.07               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            122.30             116.38 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             11.36              11.70 
[1] "0.1 - 122.3 (11.4)" "0.1 - 116.4 (11.7)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         0        5        4        6         2        10
  10Q GAIN WILD-TYPE       2        8       35       25        34        39
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           1         17         10          2        8
  10Q GAIN WILD-TYPE         2         60         45         35       29
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  5                  8
  STAGE IB                  4                 35
  STAGE II                  6                 25
  STAGE IIA                 2                 34
  STAGE IIB                10                 39
  STAGE III                 1                  2
  STAGE IIIA               17                 60
  STAGE IIIB               10                 45
  STAGE IIIC                2                 35
  STAGE IV                  8                 29
[1] 11  2
[1] TRUE
[1] "dimension of 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     4  12  34  15
  10Q GAIN WILD-TYPE  17  75 139  89
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                4                 17
  T2               12                 75
  T3               34                139
  T4               15                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED    21  15  19  10
  10Q GAIN WILD-TYPE 101  92  56  69
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               21                101
  N1               15                 92
  N2               19                 56
  N3               10                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  10Q GAIN MUTATED    60   4   2
  10Q GAIN WILD-TYPE 293  20  16
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0               60                293
  M1                4                 20
  MX                2                 16
[1] 3 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    27  39
  10Q GAIN WILD-TYPE 124 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     27   39
  10Q GAIN WILD-TYPE  124  205
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               27                124
  MALE                 39                205
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10Q GAIN MUTATED                                       9
  10Q GAIN WILD-TYPE                                    56
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                       24
  10Q GAIN WILD-TYPE                                                    133
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                                  12
  10Q GAIN WILD-TYPE                                                                57
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  10Q GAIN MUTATED                                                 15
  10Q GAIN WILD-TYPE                                               49
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10Q GAIN MUTATED                                                          2
  10Q GAIN WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  10Q GAIN MUTATED                                                           2
  10Q GAIN WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10Q GAIN MUTATED                                          1
  10Q GAIN WILD-TYPE                                        8
D20V8, multiclass
                                                                   clus
vv                                                                  10Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          24
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  10Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           133
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 57
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  64
  10Q GAIN WILD-TYPE   4 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   64
  10Q GAIN WILD-TYPE    4  325
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 2                  4
  YES               64                325
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    57   0   4   4
  10Q GAIN WILD-TYPE 261  16  14  21
D20V10, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               57                261
  R1                0                 16
  R2                4                 14
  RX                4                 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"
D20V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED      16                         2
  10Q GAIN WILD-TYPE    72                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           1    39
  10Q GAIN WILD-TYPE                                         0   204
D20V12, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                                   16                 72
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   39                204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    31  19
  11P GAIN WILD-TYPE 211 103
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                50                314 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                19                103 
$`11P GAIN MUTATED`
TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8296 
       13.12        35.24         0.95        17.49         1.32         1.48 
TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J8 TCGA-CD-8525 
       11.54        15.68        22.26        12.89        13.51         0.07 
TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-5722 
        0.10         0.13         0.10        20.02        54.08         0.99 
TCGA-D7-6526 TCGA-D7-8576 TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-7916 TCGA-FP-8099 
       17.19         6.97         2.96         7.79         3.02        17.06 
TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-A4G2 TCGA-HU-A4HD TCGA-IN-A6RJ TCGA-IN-A6RO 
        0.23         5.92        24.30        27.42         5.36         1.41 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A7C1 
        5.56         1.81         5.56        28.90         8.61        16.67 
TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 
      115.69         8.94        35.61         5.46        13.02        31.10 
TCGA-VQ-A8PJ TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y 
        2.70        64.57        14.33         1.71         8.58         9.73 
TCGA-VQ-AA68 TCGA-VQ-AA6B 
       40.08        29.98 

$`11P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.16        18.54        12.43         0.69        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        0.82         0.69        12.26         0.49        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
        0.26        12.95         0.26        16.31         1.55         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39         0.72         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44         0.59         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        1.15         0.66         3.02         0.92        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36         0.46        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        6.35         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.10         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        6.02       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.66        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85         5.95         4.14        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19         0.23        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 
       11.24        11.31        11.44         9.76        15.65         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.40         7.13         0.62        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 
       72.23        21.27         8.12         0.39        19.53        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         1.55        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10        10.62         0.76         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
        3.39        18.38         5.19        13.08         6.44         6.74 
TCGA-IN-A6RS TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        6.87         2.53        60.56         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 
       11.05         4.67       122.30        37.91        40.64       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       71.38        57.44        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       13.25        21.73        22.36        23.77         7.73        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       33.63        46.26        16.31        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A 
       23.41        15.65        19.30        23.57        59.18        28.70 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Z 
       11.70         8.68        49.25        20.81         7.36        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6J 
        8.61        55.43         4.54         6.58         5.72        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.07               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            115.69             122.30 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             9.335             11.735 
[1] "0.1 - 115.7 (9.3)"  "0.1 - 122.3 (11.7)"
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         0        2        5        2         2         8
  11P GAIN WILD-TYPE       2       11       34       29        34        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           0         11         10          7        6
  11P GAIN WILD-TYPE         3         66         45         30       31
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 11
  STAGE IB                  5                 34
  STAGE II                  2                 29
  STAGE IIA                 2                 34
  STAGE IIB                 8                 41
  STAGE III                 0                  3
  STAGE IIIA               11                 66
  STAGE IIIB               10                 45
  STAGE IIIC                7                 30
  STAGE IV                  6                 31
[1] 11  2
[1] TRUE
[1] "dimension of 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     3   7  28  15
  11P GAIN WILD-TYPE  18  80 145  89
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                3                 18
  T2                7                 80
  T3               28                145
  T4               15                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P GAIN MUTATED    12  14  18  10
  11P GAIN WILD-TYPE 110  93  57  69
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               12                110
  N1               14                 93
  N2               18                 57
  N3               10                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  11P GAIN MUTATED    49   3   4
  11P GAIN WILD-TYPE 304  21  14
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0               49                304
  M1                3                 21
  MX                4                 14
[1] 3 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    22  34
  11P GAIN WILD-TYPE 129 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     22   34
  11P GAIN WILD-TYPE  129  210
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               22                129
  MALE                 34                210
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11P GAIN MUTATED                                       6
  11P GAIN WILD-TYPE                                    59
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                       22
  11P GAIN WILD-TYPE                                                    135
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                                  13
  11P GAIN WILD-TYPE                                                                56
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  11P GAIN MUTATED                                                 12
  11P GAIN WILD-TYPE                                               52
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11P GAIN MUTATED                                                          1
  11P GAIN WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  11P GAIN MUTATED                                                           0
  11P GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11P GAIN MUTATED                                          2
  11P GAIN WILD-TYPE                                        7
D21V8, multiclass
                                                                   clus
vv                                                                  11P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  11P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  55
  11P GAIN WILD-TYPE   5 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   55
  11P GAIN WILD-TYPE    5  334
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 1                  5
  YES               55                334
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    41   2   5   4
  11P GAIN WILD-TYPE 277  14  13  21
D21V10, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               41                277
  R1                2                 14
  R2                5                 13
  RX                4                 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"
D21V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11P GAIN MUTATED      15                         1
  11P GAIN WILD-TYPE    73                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           1    32
  11P GAIN WILD-TYPE                                         0   211
D21V12, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   32                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"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    36  23
  11Q GAIN WILD-TYPE 206  99
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                59                305 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                23                 99 
$`11Q GAIN MUTATED`
TCGA-BR-6455 TCGA-BR-7704 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
       13.12        35.24         0.95        17.49         1.32         0.69 
TCGA-BR-8296 TCGA-BR-8361 TCGA-BR-8589 TCGA-BR-8686 TCGA-BR-A4IY TCGA-CD-8525 
        1.48        19.50        15.81        15.68        12.89         0.07 
TCGA-CD-8528 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 TCGA-CG-4444 
        0.10         0.13         0.10        20.02        54.08        47.05 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5722 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 
       12.00        30.97         0.99        17.19        15.22         6.97 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8099 TCGA-HU-8243 
       11.24         2.96         7.79        72.23        17.06         5.92 
TCGA-HU-A4G2 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RO 
       24.30        12.30        27.42         3.39         5.36         1.41 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-RD-A7BT 
        6.74         5.56         1.81         5.56        28.90         8.61 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       16.67       115.69         8.94        35.61         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8PJ TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91U 
       31.10         2.70        64.57        14.33         8.68         1.71 
TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-ZQ-A9CR 
        9.73         4.54        40.08        29.98         0.79 

$`11Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
        9.21        24.76        23.93        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.16        18.54        12.43         0.69        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.82        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 
       12.95         0.26        16.31         1.55         7.40         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        9.21        20.22         1.12        12.79         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        0.59         0.62        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        3.02        22.26         0.92        13.41        13.51         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 
        0.30         0.07         0.07         0.07         0.07         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        6.35         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.10         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
        8.05         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-5717 
       21.99         9.01        18.97         7.07        22.98         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
        1.02         1.02         0.99         6.02       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85         5.95 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19         0.23        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        13.71        11.31        11.44         9.76        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 
        4.34         7.40         7.13         0.62        16.24         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       14.47        21.27         8.12         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       22.29        59.54         5.03        13.58         0.56         1.55 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
        0.23        18.08        26.47         1.51        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       14.17        11.41        12.10        10.62         0.76         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       17.69         9.67         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
       18.81        18.38         5.19        13.08         6.44         6.87 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
        2.53        60.56         3.72        19.73         4.31        11.05 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        4.67       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV 
       57.44        16.87         5.79         0.92        37.74        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        19.30        23.57        59.18        28.70        11.70 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 
       49.25        20.81         7.36         8.58        44.25         8.61 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6J TCGA-ZA-A8F6 
       55.43         6.58         5.72        21.11         4.21 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.07               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            115.69             122.30 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             11.24              11.70 
[1] "0.1 - 115.7 (11.2)" "0.1 - 122.3 (11.7)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         0        3        7        2         2        10
  11Q GAIN WILD-TYPE       2       10       32       29        34        39
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           0         13         11          7        7
  11Q GAIN WILD-TYPE         3         64         44         30       30
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 10
  STAGE IB                  7                 32
  STAGE II                  2                 29
  STAGE IIA                 2                 34
  STAGE IIB                10                 39
  STAGE III                 0                  3
  STAGE IIIA               13                 64
  STAGE IIIB               11                 44
  STAGE IIIC                7                 30
  STAGE IV                  7                 30
[1] 11  2
[1] TRUE
[1] "dimension of 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     3  13  28  18
  11Q GAIN WILD-TYPE  18  74 145  86
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                3                 18
  T2               13                 74
  T3               28                145
  T4               18                 86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q GAIN MUTATED    16  17  22   8
  11Q GAIN WILD-TYPE 106  90  53  71
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               16                106
  N1               17                 90
  N2               22                 53
  N3                8                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  11Q GAIN MUTATED    59   3   3
  11Q GAIN WILD-TYPE 294  21  15
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0               59                294
  M1                3                 21
  MX                3                 15
[1] 3 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    28  37
  11Q GAIN WILD-TYPE 123 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     28   37
  11Q GAIN WILD-TYPE  123  207
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               28                123
  MALE                 37                207
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11Q GAIN MUTATED                                       6
  11Q GAIN WILD-TYPE                                    59
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                       25
  11Q GAIN WILD-TYPE                                                    132
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                                  14
  11Q GAIN WILD-TYPE                                                                55
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  11Q GAIN MUTATED                                                 16
  11Q GAIN WILD-TYPE                                               48
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11Q GAIN MUTATED                                                          1
  11Q GAIN WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  11Q GAIN MUTATED                                                           1
  11Q GAIN WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11Q GAIN MUTATED                                          1
  11Q GAIN WILD-TYPE                                        8
D22V8, multiclass
                                                                   clus
vv                                                                  11Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          25
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               14
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  11Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           132
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 55
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  64
  11Q GAIN WILD-TYPE   5 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   64
  11Q GAIN WILD-TYPE    5  325
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 1                  5
  YES               64                325
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    50   2   6   4
  11Q GAIN WILD-TYPE 268  14  12  21
D22V10, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               50                268
  R1                2                 14
  R2                6                 12
  RX                4                 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"
D22V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11Q GAIN MUTATED      15                         2
  11Q GAIN WILD-TYPE    73                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           1    37
  11Q GAIN WILD-TYPE                                         0   206
D22V12, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   37                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"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    55  20
  12P GAIN WILD-TYPE 187 102
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                75                289 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                20                102 
$`12P GAIN MUTATED`
TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-7723 TCGA-BR-7959 
       39.12        32.78         1.25        21.11        18.54        18.71 
TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 
       12.26         1.55        19.50         0.26         0.95         3.32 
TCGA-BR-8381 TCGA-BR-8486 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-CD-5798 
        0.26        20.22         0.92         0.72         1.15         2.83 
TCGA-CD-5799 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CG-4444 TCGA-CG-4460 
        3.25         0.07         0.16         0.10        47.05        21.99 
TCGA-CG-4475 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5727 TCGA-D7-5578 TCGA-D7-6518 
       22.98         0.99        12.03        79.07        12.66        19.13 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A6EX 
       18.54        17.19        11.31        19.50         5.92        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-F1-A72C TCGA-FP-7735 
        2.96        15.65         7.40        16.24         8.12         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 
       19.53        22.29         1.55         1.51        14.17        12.10 
TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GT 
       24.30         3.25        22.75        25.81         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ 
        6.25        10.19        27.42         3.45         3.39         5.36 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-RD-A8N6 
        6.44         6.74         2.53        60.56        28.90         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A91A 
        5.79        37.74        13.25        21.73         7.73        28.70 
TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A928 
        8.68        20.81         5.72 

$`12P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
       15.95        13.12        10.13        13.68         7.00         0.82 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 
        0.62        13.84        13.22        16.14         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       23.93        15.42        28.01         0.69         0.16        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69        12.76        17.49         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         0.49        20.55         0.72         0.26        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8362 
        0.26        16.31         1.48         7.40         6.18         0.36 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
       22.19         2.96        13.74         4.31        14.04         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       19.17        14.79         0.69        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        0.72         9.21         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
        1.15         0.66         3.02        22.26        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         0.79        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI 
       19.36        13.51         0.46        20.65        20.42        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       11.57         5.13        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.13         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       12.03         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        6.97         1.02         1.02         0.99         6.02       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
        7.99        12.36        11.93        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       17.85         5.95         4.14        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       10.55        12.33        24.72        16.80        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
        6.97        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.34         7.13         0.62         7.79         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       72.23        21.27         3.02        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 
       13.58         0.56         0.23        18.08        26.47         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 
       14.27        12.59        11.41        10.62         0.76         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       12.30        11.84        24.20        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.10         0.26         2.10        12.95        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 
       12.30         9.67         8.88         8.81        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT 
       18.38         5.19        13.08         1.41         6.87         5.56 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
        1.81         5.56         3.72        19.73         4.31        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         4.67        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44        35.61        16.87 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        0.92         5.46        13.02        31.10        22.36        23.77 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       19.07        33.63        46.26        16.31         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
        1.87         9.27        23.41        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91U 
       64.57        14.33        59.18        11.70        49.25         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         8.58         9.73        44.25         8.61        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        4.54         6.58        40.08        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.07               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             79.07             122.30 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             10.19              11.77 
[1] "0.1 - 79.1 (10.2)"  "0.1 - 122.3 (11.8)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         0        1        7        4        12        13
  12P GAIN WILD-TYPE       2       12       32       27        24        36
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           1         17         11          6        7
  12P GAIN WILD-TYPE         2         60         44         31       30
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 12
  STAGE IB                  7                 32
  STAGE II                  4                 27
  STAGE IIA                12                 24
  STAGE IIB                13                 36
  STAGE III                 1                  2
  STAGE IIIA               17                 60
  STAGE IIIB               11                 44
  STAGE IIIC                6                 31
  STAGE IV                  7                 30
[1] 11  2
[1] TRUE
[1] "dimension of 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     4  13  46  16
  12P GAIN WILD-TYPE  17  74 127  88
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                4                 17
  T2               13                 74
  T3               46                127
  T4               16                 88
[1] 4 2
[1] TRUE
[1] "dimension of 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   24 20 21 14
  12P GAIN WILD-TYPE 98 87 54 65
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               24                 98
  N1               20                 87
  N2               21                 54
  N3               14                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  12P GAIN MUTATED    70   5   4
  12P GAIN WILD-TYPE 283  19  14
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               70                283
  M1                5                 19
  MX                4                 14
[1] 3 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    29  50
  12P GAIN WILD-TYPE 122 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     29   50
  12P GAIN WILD-TYPE  122  194
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               29                122
  MALE                 50                194
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12P GAIN MUTATED                                      15
  12P GAIN WILD-TYPE                                    50
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                       26
  12P GAIN WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                                  13
  12P GAIN WILD-TYPE                                                                56
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  12P GAIN MUTATED                                                 17
  12P GAIN WILD-TYPE                                               47
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12P GAIN MUTATED                                                          5
  12P GAIN WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  12P GAIN MUTATED                                                           1
  12P GAIN WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12P GAIN MUTATED                                          1
  12P GAIN WILD-TYPE                                        8
D23V8, multiclass
                                                                   clus
vv                                                                  12P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  12P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  79
  12P GAIN WILD-TYPE   6 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   79
  12P GAIN WILD-TYPE    6  310
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 0                  6
  YES               79                310
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    68   3   4   1
  12P GAIN WILD-TYPE 250  13  14  24
D23V10, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               68                250
  R1                3                 13
  R2                4                 14
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12P GAIN MUTATED      20                         1
  12P GAIN WILD-TYPE    68                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           0    48
  12P GAIN WILD-TYPE                                         1   195
D23V12, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                                   20                 68
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   48                195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    47  20
  12Q GAIN WILD-TYPE 195 102
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                67                297 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                20                102 
$`12Q GAIN MUTATED`
TCGA-BR-4267 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6709 TCGA-BR-7723 TCGA-BR-7959 
        6.18        39.12        32.78         1.25        18.54        18.71 
TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8370 TCGA-BR-8381 
       12.26         1.55         0.26         0.95         3.32         0.26 
TCGA-BR-8589 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-CD-5798 TCGA-CD-5799 
       15.81         0.92         0.72         0.53         2.83         3.25 
TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4444 
        0.07         0.16         0.13         0.13         0.13        47.05 
TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5722 TCGA-CG-5727 TCGA-D7-5578 TCGA-D7-6518 
       21.99        12.00         0.99        79.07        12.66        19.13 
TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-8573 TCGA-D7-A4YV TCGA-D7-A74A 
       18.54        17.19         4.14        19.50         5.92         7.40 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-A4BF TCGA-HU-8238 TCGA-HU-8249 
        8.12         3.02        22.29         1.55         1.51        14.17 
TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GT 
       12.10        24.30         3.25        22.75         8.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8663 
        6.25        10.19        17.69        27.42         3.45         3.39 
TCGA-IN-A6RJ TCGA-IP-7968 TCGA-KB-A6F7 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT 
        5.36         2.53        60.56         8.94         5.79        37.74 
TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91X 
        7.73         2.70        14.33         8.68        20.81         8.58 
TCGA-VQ-A928 
        5.72 

$`12Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
       13.12        10.13        13.68         7.00         0.82         0.62 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.84        13.22        16.14         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       23.93        15.42        28.01         0.69         0.16        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69        12.76        17.49         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
        0.69         0.49        20.55         0.72         0.26        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.26        16.31         1.48         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        0.36        22.19         2.96        13.74         4.31        14.04 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 
        0.36        19.17        14.79         0.69        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39         0.72         9.21        20.22         1.12        12.79 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       15.81        16.44         0.59        15.68         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU 
       12.56         1.15         0.66         3.02        22.26        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51        12.89         0.79        14.17        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       13.64        11.57         5.13        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         6.35         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 
       54.08         4.01        14.01        29.98        19.07        12.03 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
        9.01        18.97         7.07        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 
        1.02         1.02         0.99         6.02       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
        7.99        12.36        11.93        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
       17.85         5.95        15.22        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 
       11.31        12.33        24.72        16.80        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YX 
        6.97        21.14        20.91        14.27        16.44        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 
        9.76         2.96        15.65         4.34         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.79        16.24         6.58        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        0.39        19.53        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
        0.56         0.23        18.08        26.47         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.59        11.41        10.62         0.76         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
        0.10         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI 
        9.67         8.88         8.81        21.21        18.81        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         6.44         6.74         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56         1.81         5.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.31        11.05         8.61         4.67        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       35.61        16.87         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       31.10        21.73        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        19.30        23.57        64.57        59.18        28.70 
TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
       11.70        49.25         1.71         7.36         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6B 
        8.61        55.43         4.54         6.58        40.08        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11         4.21         0.79 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             79.07             122.30 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               7.4               12.3 
[1] "0.1 - 79.1 (7.4)"   "0.1 - 122.3 (12.3)"
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0        0        4        5         9        11
  12Q GAIN WILD-TYPE       2       13       35       26        27        38
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           1         15         12          4        8
  12Q GAIN WILD-TYPE         2         62         43         33       29
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 13
  STAGE IB                  4                 35
  STAGE II                  5                 26
  STAGE IIA                 9                 27
  STAGE IIB                11                 38
  STAGE III                 1                  2
  STAGE IIIA               15                 62
  STAGE IIIB               12                 43
  STAGE IIIC                4                 33
  STAGE IV                  8                 29
[1] 11  2
[1] TRUE
[1] "dimension of 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     2  11  39  17
  12Q GAIN WILD-TYPE  19  76 134  87
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                2                 19
  T2               11                 76
  T3               39                134
  T4               17                 87
[1] 4 2
[1] TRUE
[1] "dimension of 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    17  18  23  11
  12Q GAIN WILD-TYPE 105  89  52  68
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               17                105
  N1               18                 89
  N2               23                 52
  N3               11                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  12Q GAIN MUTATED    61   5   3
  12Q GAIN WILD-TYPE 292  19  15
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               61                292
  M1                5                 19
  MX                3                 15
[1] 3 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    24  45
  12Q GAIN WILD-TYPE 127 199
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     24   45
  12Q GAIN WILD-TYPE  127  199
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               24                127
  MALE                 45                199
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12Q GAIN MUTATED                                      15
  12Q GAIN WILD-TYPE                                    50
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                       20
  12Q GAIN WILD-TYPE                                                    137
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                                  11
  12Q GAIN WILD-TYPE                                                                58
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  12Q GAIN MUTATED                                                 16
  12Q GAIN WILD-TYPE                                               48
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12Q GAIN MUTATED                                                          3
  12Q GAIN WILD-TYPE                                                       18
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  12Q GAIN MUTATED                                                           2
  12Q GAIN WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12Q GAIN MUTATED                                          1
  12Q GAIN WILD-TYPE                                        8
D24V8, multiclass
                                                                   clus
vv                                                                  12Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           15
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  12Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             50
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  69
  12Q GAIN WILD-TYPE   6 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   69
  12Q GAIN WILD-TYPE    6  320
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 0                  6
  YES               69                320
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    54   3   4   2
  12Q GAIN WILD-TYPE 264  13  14  23
D24V10, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               54                264
  R1                3                 13
  R2                4                 14
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12Q GAIN MUTATED      23                         0
  12Q GAIN WILD-TYPE    65                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           0    36
  12Q GAIN WILD-TYPE                                         1   207
D24V12, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                                   23                 65
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   36                207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    89  38
  13Q GAIN WILD-TYPE 153  84
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               127                237 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                38                 84 
$`13Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6563 
       11.70         4.64         9.57         6.61        15.95        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-7197 TCGA-BR-7704 
        0.62        32.78        13.84        21.11         9.21        35.24 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8286 
        0.69        18.54         0.69        12.26         0.49        12.95 
TCGA-BR-8362 TCGA-BR-8373 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8588 
        0.36        14.79        15.85         5.39         9.21        12.79 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U 
       11.54        16.44        15.68         0.62        10.68         1.15 
TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4J9 
       22.26         0.72        14.17        12.82        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-5800 
       20.65        20.42         1.15         5.13         3.25        13.15 
TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
        0.07         0.13         0.13         0.13         0.07         0.10 
TCGA-CG-4300 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4469 
       20.02        15.95         7.99        54.08        47.05         7.07 
TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 
       12.00         1.02         4.01        55.04         7.99        12.36 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       12.66        19.13        18.54        17.85        17.19         4.14 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-A4YT 
       15.98        10.55        11.31        19.50        17.19        14.27 
TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 
       14.76        11.24         2.96        15.65         0.62         7.79 
TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       72.23        19.53         1.55        12.59        14.17        12.10 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU 
       12.30        11.84        22.75        25.81         6.51         6.25 
TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI 
        0.26        19.36        17.69        12.30        27.42        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
        5.19         1.41         6.44         1.81         5.56        28.90 
TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 
        4.31         8.61       122.30        37.91       115.69        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
        8.94        35.61         5.79        37.74         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PY 
       13.02        21.73         2.70        17.85        23.41        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A922 TCGA-VQ-AA6B 
       59.18        28.70        20.81         1.71         8.61        29.98 
TCGA-VQ-AA6J 
       21.11 

$`13Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62         6.61         6.97         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 
        6.18        34.68        13.12        10.13        13.68         7.00 
TCGA-BR-6564 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
        0.82        13.22        16.14         1.25         8.98        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       31.20        32.94        12.82        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
       28.01         0.16        12.43         0.95         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8284 
       18.71        17.49         0.82         1.32        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.26         0.26        16.31         1.55         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 
        0.69         0.26         3.72         0.72        20.22         1.12 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       15.81         0.59        12.56         0.66         3.02         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J4 TCGA-BR-A4J6 
       13.41        13.51        12.89         0.79         0.53         0.66 
TCGA-BR-A4J7 TCGA-BR-A4QI TCGA-BR-A4QL TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 
       19.36        13.64        11.57         2.83        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.10         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         6.35         0.13 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        0.13         0.13         0.10         0.10         3.02        27.02 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        1.02         8.05         4.01        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
       12.03        21.99         9.01        18.97        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        6.97         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5733 
       12.03        15.02        28.96        79.07        65.10        21.07 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6528 
       11.93        20.55        18.84        18.61         5.95        15.22 
TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8575 TCGA-D7-8576 
       12.79        12.33        24.72        16.80         0.23         6.97 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       21.14        20.91        16.44         5.92        15.16        13.78 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A 
       13.71        11.31        11.44         9.76         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13        16.24         6.58        14.47        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
        0.39         3.02        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
       13.58         0.56         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
        5.92        14.27        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        5.59        24.20         3.25        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GX TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 
        8.98         0.10        10.19         2.10        12.95         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IP-7968 
        5.36        13.08         6.74         6.87         5.56         2.53 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 
       60.56         3.72        19.73        11.05         4.67        16.67 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8E2 
       40.64       116.38        71.38        16.87         0.92        31.10 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
       16.31         1.87         9.27        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A91X 
       64.57        11.70         8.68        49.25         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73        44.25        55.43         4.54         6.58         5.72 
TCGA-VQ-AA68 TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08         4.21         0.79 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.07               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            122.30             116.38 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             12.59               9.76 
[1] "0.1 - 122.3 (12.6)" "0.1 - 116.4 (9.8)" 
[1] "hr=" "1.3"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         1        3       10       11        14        18
  13Q GAIN WILD-TYPE       1       10       29       20        22        31
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           1         29         18         10       16
  13Q GAIN WILD-TYPE         2         48         37         27       21
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  3                 10
  STAGE IB                 10                 29
  STAGE II                 11                 20
  STAGE IIA                14                 22
  STAGE IIB                18                 31
  STAGE III                 1                  2
  STAGE IIIA               29                 48
  STAGE IIIB               18                 37
  STAGE IIIC               10                 27
  STAGE IV                 16                 21
[1] 11  2
[1] TRUE
[1] "dimension of 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     5  35  59  34
  13Q GAIN WILD-TYPE  16  52 114  70
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                5                 16
  T2               35                 52
  T3               59                114
  T4               34                 70
[1] 4 2
[1] TRUE
[1] "dimension of 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   40 36 29 28
  13Q GAIN WILD-TYPE 82 71 46 51
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               40                 82
  N1               36                 71
  N2               29                 46
  N3               28                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  13Q GAIN MUTATED   129   7   2
  13Q GAIN WILD-TYPE 224  17  16
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0              129                224
  M1                7                 17
  MX                2                 16
[1] 3 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    47  91
  13Q GAIN WILD-TYPE 104 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     47   91
  13Q GAIN WILD-TYPE  104  153
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               47                104
  MALE                 91                153
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  13Q GAIN MUTATED                                      16
  13Q GAIN WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                       53
  13Q GAIN WILD-TYPE                                                    104
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                                  27
  13Q GAIN WILD-TYPE                                                                42
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  13Q GAIN MUTATED                                                 23
  13Q GAIN WILD-TYPE                                               41
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  13Q GAIN MUTATED                                                         10
  13Q GAIN WILD-TYPE                                                       11
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  13Q GAIN MUTATED                                                           5
  13Q GAIN WILD-TYPE                                                         3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  13Q GAIN MUTATED                                          3
  13Q GAIN WILD-TYPE                                        6
D25V8, multiclass
                                                                   clus
vv                                                                  13Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          53
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                23
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  13Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           104
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 42
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  41
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1 137
  13Q GAIN WILD-TYPE   5 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1  137
  13Q GAIN WILD-TYPE    5  252
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 1                  5
  YES              137                252
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED   110   7   6   9
  13Q GAIN WILD-TYPE 208   9  12  16
D25V10, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0              110                208
  R1                7                  9
  R2                6                 12
  RX                9                 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"
D25V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  13Q GAIN MUTATED      31                         3
  13Q GAIN WILD-TYPE    57                         3
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           1    83
  13Q GAIN WILD-TYPE                                         0   160
D25V12, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                                   31                 57
  BLACK OR AFRICAN AMERICAN                                3                  3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   83                160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    10  11
  14Q GAIN WILD-TYPE 232 111
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                343 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                111 
$`14Q GAIN MUTATED`
TCGA-BR-4187 TCGA-BR-6705 TCGA-BR-8060 TCGA-BR-8295 TCGA-BR-A4J8 TCGA-BR-A4PE 
        4.64        13.84         1.32         1.55        13.51        20.42 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CG-4444 TCGA-CG-4460 TCGA-D7-6518 TCGA-D7-A6F2 
        0.13         0.13        47.05        21.99        19.13        15.65 
TCGA-EQ-5647 TCGA-FP-A4BF TCGA-HU-8243 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A7NT 
        0.62         1.55         5.92        18.38         1.41         5.56 
TCGA-RD-A7BS TCGA-VQ-A925 TCGA-VQ-AA68 
       11.05         4.54        40.08 

$`14Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         6.97         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.62        32.78        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49         0.82         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         0.72         0.26        12.95         0.26        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.48         7.40         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39         0.72         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         0.59 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         0.62        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        3.02        22.26         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       19.36         0.46        20.65         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.10         6.35         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
        7.99        12.36        12.66        11.93        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       18.54        18.61        17.85         5.95        17.19         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19         0.23         6.97 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
        9.76         2.96         4.34         7.40         7.13         7.79 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
       16.24         6.58        14.47        72.23        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39        19.53         3.02        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39         5.36         5.19        13.08         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.74         6.87         1.81         2.53         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7BW 
       28.90         3.72        19.73         4.31         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        37.74         5.46        13.25        13.02        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        19.30        23.57        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       59.18        28.70        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71         7.36         8.58         9.73        44.25         8.61 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
       55.43         6.58         5.72        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.13               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             47.05             122.30 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              5.92              11.70 
[1] "0.1 - 47.0 (5.9)"   "0.1 - 122.3 (11.7)"
[1] "hr=" "1.9"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         0        1        3        0         1         3
  14Q GAIN WILD-TYPE       2       12       36       31        35        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           0          6          2          3        2
  14Q GAIN WILD-TYPE         3         71         53         34       35
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 12
  STAGE IB                  3                 36
  STAGE II                  0                 31
  STAGE IIA                 1                 35
  STAGE IIB                 3                 46
  STAGE III                 0                  3
  STAGE IIIA                6                 71
  STAGE IIIB                2                 53
  STAGE IIIC                3                 34
  STAGE IV                  2                 35
[1] 11  2
[1] TRUE
[1] "dimension of 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     2   5   8   6
  14Q GAIN WILD-TYPE  19  82 165  98
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                2                 19
  T2                5                 82
  T3                8                165
  T4                6                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q GAIN MUTATED     6   4   4   7
  14Q GAIN WILD-TYPE 116 103  71  72
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                6                116
  N1                4                103
  N2                4                 71
  N3                7                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  14Q GAIN MUTATED    20   2   0
  14Q GAIN WILD-TYPE 333  22  18
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0               20                333
  M1                2                 22
  MX                0                 18
[1] 3 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    10  12
  14Q GAIN WILD-TYPE 141 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     10   12
  14Q GAIN WILD-TYPE  141  232
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               10                141
  MALE                 12                232
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  14Q GAIN MUTATED                                       4
  14Q GAIN WILD-TYPE                                    61
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                       12
  14Q GAIN WILD-TYPE                                                    145
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                                   1
  14Q GAIN WILD-TYPE                                                                68
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  14Q GAIN MUTATED                                                  4
  14Q GAIN WILD-TYPE                                               60
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  14Q GAIN MUTATED                                                          0
  14Q GAIN WILD-TYPE                                                       21
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  14Q GAIN MUTATED                                                           0
  14Q GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  14Q GAIN MUTATED                                          1
  14Q GAIN WILD-TYPE                                        8
D26V8, multiclass
                                                                   clus
vv                                                                  14Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  14Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           145
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  60
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  22
  14Q GAIN WILD-TYPE   6 367
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   22
  14Q GAIN WILD-TYPE    6  367
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 0                  6
  YES               22                367
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    14   2   3   1
  14Q GAIN WILD-TYPE 304  14  15  24
D26V10, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               14                304
  R1                2                 14
  R2                3                 15
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  14Q GAIN MUTATED       4                         0
  14Q GAIN WILD-TYPE    84                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           0    16
  14Q GAIN WILD-TYPE                                         1   227
D26V12, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                                    4                 84
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   16                227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    17  16
  15Q GAIN WILD-TYPE 225 106
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                33                331 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                16                106 
$`15Q GAIN MUTATED`
TCGA-BR-4183 TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7959 TCGA-BR-8683 TCGA-BR-8687 
        6.61         1.25         9.21        18.71         0.59         0.62 
TCGA-BR-A4J4 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-A486 TCGA-CG-4477 
        0.53         1.15         3.25         0.07         6.35        30.97 
TCGA-CG-5727 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6815 TCGA-EQ-5647 TCGA-F1-6875 
       79.07        18.84         5.95        15.98         0.62        72.23 
TCGA-F1-A72C TCGA-FP-8099 TCGA-HU-A4GH TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RO 
        8.12        17.06        11.77         3.45         3.39         1.41 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A8MV TCGA-VQ-A8DZ TCGA-VQ-A8PC 
       60.56        28.90         8.61       122.30        13.02        46.26 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A925 
        2.70        17.85         4.54 

$`15Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        0.62        32.78        13.84        13.22        16.14         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       21.11        30.90        31.20        32.94        12.82        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
       18.54        12.43         0.95         0.69        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26        12.95         0.26        16.31         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.48         7.40         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39         0.72         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        7.53         0.49        11.54        15.81        16.44        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
        0.92        13.41        13.51        12.89         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 
       14.17        12.82         0.66        19.36        13.51         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42        13.64        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.13         0.10         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97         1.02         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 
        0.99       105.07        12.03        15.02        28.96        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        20.55        18.54        18.61        17.85 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19         4.14        15.22        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
        6.97        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76         2.96        15.65         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        7.13         7.79        16.24         6.58        14.47        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        0.39        19.53         3.02        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         0.56         1.55         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 
        9.67         8.88         8.81        27.42        21.21        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.38         5.36         5.19        13.08         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG 
        6.87         5.56         1.81         2.53         5.56         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW 
       19.73         4.31        11.05         4.67        16.67        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       35.61        16.87         5.79         0.92        37.74         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        31.10        21.73        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       19.07        33.63        16.31         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       28.70        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         8.58         9.73        44.25         8.61        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        6.58         5.72        40.08        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.07               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            122.30             116.38 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              8.12              11.84 
[1] "0.1 - 122.3 (8.1)"  "0.1 - 116.4 (11.8)"
[1] "hr=" "1.4"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         0        3        2        3         3         3
  15Q GAIN WILD-TYPE       2       10       37       28        33        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           1          7          6          2        5
  15Q GAIN WILD-TYPE         2         70         49         35       32
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 10
  STAGE IB                  2                 37
  STAGE II                  3                 28
  STAGE IIA                 3                 33
  STAGE IIB                 3                 46
  STAGE III                 1                  2
  STAGE IIIA                7                 70
  STAGE IIIB                6                 49
  STAGE IIIC                2                 35
  STAGE IV                  5                 32
[1] 11  2
[1] TRUE
[1] "dimension of 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     3   7  15  10
  15Q GAIN WILD-TYPE  18  80 158  94
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                3                 18
  T2                7                 80
  T3               15                158
  T4               10                 94
[1] 4 2
[1] TRUE
[1] "dimension of 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     9   7  12   7
  15Q GAIN WILD-TYPE 113 100  63  72
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                9                113
  N1                7                100
  N2               12                 63
  N3                7                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  15Q GAIN MUTATED    29   5   1
  15Q GAIN WILD-TYPE 324  19  17
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               29                324
  M1                5                 19
  MX                1                 17
[1] 3 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    10  25
  15Q GAIN WILD-TYPE 141 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     10   25
  15Q GAIN WILD-TYPE  141  219
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               10                141
  MALE                 25                219
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  15Q GAIN MUTATED                                       4
  15Q GAIN WILD-TYPE                                    61
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                       12
  15Q GAIN WILD-TYPE                                                    145
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                                   8
  15Q GAIN WILD-TYPE                                                                61
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  15Q GAIN MUTATED                                                  7
  15Q GAIN WILD-TYPE                                               57
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  15Q GAIN MUTATED                                                          2
  15Q GAIN WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  15Q GAIN MUTATED                                                           0
  15Q GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  15Q GAIN MUTATED                                          2
  15Q GAIN WILD-TYPE                                        7
D27V8, multiclass
                                                                   clus
vv                                                                  15Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          12
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  15Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           145
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  35
  15Q GAIN WILD-TYPE   6 354
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   35
  15Q GAIN WILD-TYPE    6  354
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                  6
  YES               35                354
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    23   2   6   1
  15Q GAIN WILD-TYPE 295  14  12  24
D27V10, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               23                295
  R1                2                 14
  R2                6                 12
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  15Q GAIN MUTATED       9                         2
  15Q GAIN WILD-TYPE    79                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           1    17
  15Q GAIN WILD-TYPE                                         0   226
D27V12, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                                    9                 79
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   17                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"

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    31  14
  16P GAIN WILD-TYPE 211 108
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                45                319 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                14                108 
$`16P GAIN MUTATED`
TCGA-BR-4187 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-8080 TCGA-BR-8484 TCGA-BR-8486 
        4.64        10.13         0.62         0.49         0.72        20.22 
TCGA-BR-A452 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-CD-5801 TCGA-CD-8528 
        0.66        12.82        13.51        20.65        13.18         0.10 
TCGA-CD-8529 TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-4475 
        0.13        54.08        47.05        21.99        12.00        22.98 
TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6817 
        1.02         0.99         4.01        18.54        17.19        12.79 
TCGA-D7-6818 TCGA-D7-8576 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
       10.55         6.97         0.39         3.02        22.29        17.06 
TCGA-FP-8631 TCGA-FP-A8CX TCGA-HU-8249 TCGA-HU-A4GP TCGA-HU-A4GY TCGA-IN-8663 
        0.56         0.23        14.17         8.98         0.26         3.39 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        5.19         1.41         6.44         5.56         1.81         2.53 
TCGA-RD-A7BT TCGA-VQ-A925 TCGA-VQ-AA6B 
        8.61         4.54        29.98 

$`16P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         6.97         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.12        13.68         7.00        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.54        12.43         0.95         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
       17.49         0.82         1.32         0.69        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 
        0.72         0.26        12.95         0.26        16.31         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.48         7.40         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 
       15.85         3.72         5.39         9.21         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        12.56         1.15         3.02        22.26         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         0.79         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF 
        0.53         0.66        19.36         0.46        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.35         0.13         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.10         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99         8.05         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        19.07        12.03         9.01        18.97         7.07 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
       30.97         6.97         1.02         0.99         6.02       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
       12.03        15.02        28.96        79.07        65.10        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       20.55        18.84        18.61        17.85         5.95         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.22        15.98        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19         0.23        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 
        6.58        14.47        72.23        21.27         8.12        19.53 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
       59.54         5.03        13.58         1.55        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        14.27        12.59        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H0 
       29.98         0.10         6.51         6.25        10.19         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        17.69        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
        8.81        27.42        21.21         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A6F7 
        5.36        13.08         6.74         6.87         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW 
       28.90         3.72        19.73         4.31        11.05         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        37.74         5.46        13.25        13.02        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        19.30        23.57        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       59.18        28.70        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71         7.36         8.58         9.73        44.25         8.61 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 
       55.43         6.58         5.72        40.08        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.10               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             54.08             122.30 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              6.44              12.03 
[1] "0.1 - 54.1 (6.4)"   "0.1 - 122.3 (12.0)"
[1] "hr=" "1.2"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         0        2        2        0         3         5
  16P GAIN WILD-TYPE       2       11       37       31        33        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           0         17          4          6       10
  16P GAIN WILD-TYPE         3         60         51         31       27
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 11
  STAGE IB                  2                 37
  STAGE II                  0                 31
  STAGE IIA                 3                 33
  STAGE IIB                 5                 44
  STAGE III                 0                  3
  STAGE IIIA               17                 60
  STAGE IIIB                4                 51
  STAGE IIIC                6                 31
  STAGE IV                 10                 27
[1] 11  2
[1] TRUE
[1] "dimension of 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     3  10  19  17
  16P GAIN WILD-TYPE  18  77 154  87
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                3                 18
  T2               10                 77
  T3               19                154
  T4               17                 87
[1] 4 2
[1] TRUE
[1] "dimension of 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    11  14  12  12
  16P GAIN WILD-TYPE 111  93  63  67
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               11                111
  N1               14                 93
  N2               12                 63
  N3               12                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16P GAIN MUTATED    37   6   8
  16P GAIN WILD-TYPE 316  18  10
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               37                316
  M1                6                 18
  MX                8                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    19  32
  16P GAIN WILD-TYPE 132 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     19   32
  16P GAIN WILD-TYPE  132  212
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               19                132
  MALE                 32                212
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16P GAIN MUTATED                                       8
  16P GAIN WILD-TYPE                                    57
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                       23
  16P GAIN WILD-TYPE                                                    134
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                                   8
  16P GAIN WILD-TYPE                                                                61
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  16P GAIN MUTATED                                                  6
  16P GAIN WILD-TYPE                                               58
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16P GAIN MUTATED                                                          3
  16P GAIN WILD-TYPE                                                       18
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  16P GAIN MUTATED                                                           0
  16P GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16P GAIN MUTATED                                          1
  16P GAIN WILD-TYPE                                        8
D28V8, multiclass
                                                                   clus
vv                                                                  16P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  16P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     3  48
  16P GAIN WILD-TYPE   3 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3   48
  16P GAIN WILD-TYPE    3  341
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 3                  3
  YES               48                341
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    41   0   6   3
  16P GAIN WILD-TYPE 277  16  12  22
D28V10, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               41                277
  R1                0                 16
  R2                6                 12
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16P GAIN MUTATED      11                         1
  16P GAIN WILD-TYPE    77                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           1    28
  16P GAIN WILD-TYPE                                         0   215
D28V12, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                                   11                 77
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   28                215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    21  14
  16Q GAIN WILD-TYPE 221 108
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                35                329 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                14                108 
$`16Q GAIN MUTATED`
TCGA-BR-4187 TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J5 TCGA-BR-A4J8 
        4.64        20.22         0.66         0.92        12.82        13.51 
TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8529 TCGA-CG-4438 TCGA-CG-4460 TCGA-CG-4472 
       13.18         0.10         0.13        54.08        21.99        12.00 
TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-6521 TCGA-D7-6818 TCGA-D7-8576 
        1.02         0.99         4.01        18.54        10.55         6.97 
TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 
        7.79         0.39         3.02        22.29        17.06         0.56 
TCGA-FP-A8CX TCGA-HU-8249 TCGA-IN-8663 TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
        0.23        14.17         3.39         1.41         6.44         6.74 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-RD-A7BT TCGA-VQ-A8DV TCGA-VQ-AA6B 
        5.56         1.81         8.61        13.25        29.98 

$`16Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         6.97         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         0.49        20.55         0.72         0.26        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.26        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       14.79         0.69         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        0.72         9.21         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        1.15         3.02        22.26        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79         0.72        14.17         0.53         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.07         0.07         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.13         0.13         0.10         6.35         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        7.99         8.05         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 
       19.07        12.03         9.01        18.97         7.07        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
       30.97         6.97         1.02         0.99         6.02       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
       12.03        15.02        28.96        79.07        65.10        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85         5.95        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-6822 
        4.14        15.22        15.98        12.79        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19         0.23        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         4.34         7.40         7.13         0.62 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
       16.24         6.58        14.47        72.23        21.27         8.12 
TCGA-FP-7829 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-HF-A5NB 
       19.53        59.54         5.03        13.58         1.55        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.30         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
        3.45        18.81        18.38         5.36         5.19        13.08 
TCGA-IN-A6RS TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
        6.87         2.53         5.56        60.56        28.90         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
       19.73         4.31        11.05         4.67        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        13.02        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ 
        7.73        19.07        33.63        46.26        16.31         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       23.57        64.57        14.33        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
        8.68        49.25        20.81         1.71         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73        44.25         8.61        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        40.08        21.11         4.21         0.79 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.10               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             54.08             122.30 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              6.74              11.93 
[1] "0.1 - 54.1 (6.7)"   "0.1 - 122.3 (11.9)"
[1] "hr=" "1.6"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0        2        3        0         2         2
  16Q GAIN WILD-TYPE       2       11       36       31        34        47
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           0         12          2          6       10
  16Q GAIN WILD-TYPE         3         65         53         31       27
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 11
  STAGE IB                  3                 36
  STAGE II                  0                 31
  STAGE IIA                 2                 34
  STAGE IIB                 2                 47
  STAGE III                 0                  3
  STAGE IIIA               12                 65
  STAGE IIIB                2                 53
  STAGE IIIC                6                 31
  STAGE IV                 10                 27
[1] 11  2
[1] TRUE
[1] "dimension of 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     3   7  16  13
  16Q GAIN WILD-TYPE  18  80 157  91
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                3                 18
  T2                7                 80
  T3               16                157
  T4               13                 91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16Q GAIN MUTATED    10  10   8  11
  16Q GAIN WILD-TYPE 112  97  67  68
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               10                112
  N1               10                 97
  N2                8                 67
  N3               11                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16Q GAIN MUTATED    27   6   8
  16Q GAIN WILD-TYPE 326  18  10
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               27                326
  M1                6                 18
  MX                8                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    14  27
  16Q GAIN WILD-TYPE 137 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     14   27
  16Q GAIN WILD-TYPE  137  217
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               14                137
  MALE                 27                217
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16Q GAIN MUTATED                                       5
  16Q GAIN WILD-TYPE                                    60
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                       19
  16Q GAIN WILD-TYPE                                                    138
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                                  10
  16Q GAIN WILD-TYPE                                                                59
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  16Q GAIN MUTATED                                                  3
  16Q GAIN WILD-TYPE                                               61
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16Q GAIN MUTATED                                                          2
  16Q GAIN WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  16Q GAIN MUTATED                                                           0
  16Q GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16Q GAIN MUTATED                                          1
  16Q GAIN WILD-TYPE                                        8
D29V8, multiclass
                                                                   clus
vv                                                                  16Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  16Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  61
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2  39
  16Q GAIN WILD-TYPE   4 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   39
  16Q GAIN WILD-TYPE    4  350
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 2                  4
  YES               39                350
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    31   0   5   3
  16Q GAIN WILD-TYPE 287  16  13  22
D29V10, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               31                287
  R1                0                 16
  R2                5                 13
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16Q GAIN MUTATED       9                         1
  16Q GAIN WILD-TYPE    79                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           1    22
  16Q GAIN WILD-TYPE                                         0   221
D29V12, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                                    9                 79
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   22                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    12  10
  17P GAIN WILD-TYPE 230 112
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                342 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                10                112 
$`17P GAIN MUTATED`
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8686 TCGA-BR-A4QI TCGA-CG-4455 TCGA-CG-4460 
        0.82         1.32        15.68        13.64        12.03        21.99 
TCGA-CG-4475 TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-6817 TCGA-D7-8573 TCGA-D7-A6EY 
       22.98         0.99        12.03        12.79        19.50        11.44 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7829 TCGA-HJ-7597 TCGA-HU-A4GF 
        0.62        16.24        72.23        19.53        26.47        25.81 
TCGA-HU-A4HD TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       27.42        44.25         8.61         4.54 

$`17P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.25         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       28.01         0.69         0.16        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 
        0.69        12.76        18.71        17.49         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49        20.55         0.72         0.26        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         1.55         1.48         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         0.59         0.62        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         0.79         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
        1.15        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.13         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       19.07         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 
        6.97         1.02         1.02         0.99         6.02       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       17.19         4.14        15.22        15.98        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       12.33        24.72        16.80        17.19         0.23         6.97 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.31         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
        2.96        15.65         4.34         7.40         7.13         7.79 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
        6.58        14.47        21.27         8.12         0.39         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        1.55         0.23        18.08         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       12.59        14.17        11.41        12.10        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        17.69        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.19        13.08         1.41         6.44         6.74         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        5.56         1.81         2.53         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        37.74         5.46        13.25        13.02        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        19.30        23.57        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       59.18        28.70        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 
        1.71         7.36         8.58         9.73        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        40.08        29.98        21.11         4.21         0.79 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.62               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             72.23             122.30 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             14.66              11.31 
[1] "0.6 - 72.2 (14.7)"  "0.1 - 122.3 (11.3)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         0        1        1        1         4         3
  17P GAIN WILD-TYPE       2       12       38       30        32        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           1          4          3          0        5
  17P GAIN WILD-TYPE         2         73         52         37       32
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 12
  STAGE IB                  1                 38
  STAGE II                  1                 30
  STAGE IIA                 4                 32
  STAGE IIB                 3                 46
  STAGE III                 1                  2
  STAGE IIIA                4                 73
  STAGE IIIB                3                 52
  STAGE IIIC                0                 37
  STAGE IV                  5                 32
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   5  13   6
  17P GAIN WILD-TYPE  21  82 160  98
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                0                 21
  T2                5                 82
  T3               13                160
  T4                6                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P GAIN MUTATED     6   9   4   4
  17P GAIN WILD-TYPE 116  98  71  75
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                6                116
  N1                9                 98
  N2                4                 71
  N3                4                 75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  17P GAIN MUTATED    17   4   3
  17P GAIN WILD-TYPE 336  20  15
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               17                336
  M1                4                 20
  MX                3                 15
[1] 3 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     9  15
  17P GAIN WILD-TYPE 142 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      9   15
  17P GAIN WILD-TYPE  142  229
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                9                142
  MALE                 15                229
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17P GAIN MUTATED                                       1
  17P GAIN WILD-TYPE                                    64
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                        7
  17P GAIN WILD-TYPE                                                    150
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                                   3
  17P GAIN WILD-TYPE                                                                66
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  17P GAIN MUTATED                                                  9
  17P GAIN WILD-TYPE                                               55
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17P GAIN MUTATED                                                          2
  17P GAIN WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  17P GAIN MUTATED                                                           0
  17P GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17P GAIN MUTATED                                          1
  17P GAIN WILD-TYPE                                        8
D30V8, multiclass
                                                                   clus
vv                                                                  17P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           7
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  17P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           150
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  23
  17P GAIN WILD-TYPE   5 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   23
  17P GAIN WILD-TYPE    5  366
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 1                  5
  YES               23                366
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    18   0   5   1
  17P GAIN WILD-TYPE 300  16  13  24
D30V10, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               18                300
  R1                0                 16
  R2                5                 13
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17P GAIN MUTATED       3                         1
  17P GAIN WILD-TYPE    85                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0    14
  17P GAIN WILD-TYPE                                         1   229
D30V12, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                                    3                 85
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                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"

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    31  18
  17Q GAIN WILD-TYPE 211 104
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                49                315 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                104 
$`17Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8296 
       11.70         0.82         1.32        12.95         0.26         1.48 
TCGA-BR-8369 TCGA-BR-8686 TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4QI 
       14.04        15.68        12.89         0.53        20.42        13.64 
TCGA-CD-A486 TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5719 
        6.35         7.99        12.03        21.99        22.98         1.02 
TCGA-CG-5722 TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-8573 
        0.99        12.03        18.54         5.95        12.79        19.50 
TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7829 
       11.44         2.96         0.62        16.24        72.23        19.53 
TCGA-FP-7916 TCGA-HJ-7597 TCGA-HU-8604 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI 
        3.02        26.47        12.10        27.42        18.81        18.38 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-VQ-A8DV 
        5.19         1.41         6.44         5.56         1.81        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       13.02        59.18        20.81        44.25         8.61         4.54 
TCGA-VQ-AA68 
       40.08 

$`17Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62         6.61         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       12.76        18.71        17.49         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8297 
       20.55         0.72         0.26        16.31         1.55         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        13.74         4.31         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       14.79         0.69         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.72         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44         0.59         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
        1.15         0.66         3.02        22.26         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 
       13.51         0.79         0.72        14.17        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QL 
       19.36        13.51         0.46        20.65         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         0.13         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.10         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       29.98        47.05        19.07         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       12.00        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       19.13        20.55        18.84        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14        15.22        15.98        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        17.19         0.23         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F2 
       14.76        13.71        11.24        11.31         9.76        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        4.34         7.40         7.13         7.79         6.58        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
       21.27         8.12         0.39        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         1.55         0.23        18.08 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
        9.67         8.88         8.81        21.21         3.45         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IP-7968 TCGA-KB-A6F5 
        5.36        13.08         6.74         6.87         2.53         5.56 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
       60.56        28.90         3.72        19.73         4.31        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        8.61         4.67        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 
       16.87         5.79         0.92        37.74         5.46        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        19.30        23.57        64.57        14.33 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W 
       28.70        11.70         8.68        49.25         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B 
        8.58         9.73        55.43         6.58         5.72        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11         4.21         0.79 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.26               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             72.23             122.30 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             12.10              11.31 
[1] "0.3 - 72.2 (12.1)"  "0.1 - 122.3 (11.3)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         0        2        7        3         5         5
  17Q GAIN WILD-TYPE       2       11       32       28        31        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           1          8          5          5        9
  17Q GAIN WILD-TYPE         2         69         50         32       28
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 11
  STAGE IB                  7                 32
  STAGE II                  3                 28
  STAGE IIA                 5                 31
  STAGE IIB                 5                 44
  STAGE III                 1                  2
  STAGE IIIA                8                 69
  STAGE IIIB                5                 50
  STAGE IIIC                5                 32
  STAGE IV                  9                 28
[1] 11  2
[1] TRUE
[1] "dimension of 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     3  14  20  14
  17Q GAIN WILD-TYPE  18  73 153  90
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                3                 18
  T2               14                 73
  T3               20                153
  T4               14                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q GAIN MUTATED    18  12   8  12
  17Q GAIN WILD-TYPE 104  95  67  67
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               18                104
  N1               12                 95
  N2                8                 67
  N3               12                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  17Q GAIN MUTATED    40   7   4
  17Q GAIN WILD-TYPE 313  17  14
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               40                313
  M1                7                 17
  MX                4                 14
[1] 3 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    18  33
  17Q GAIN WILD-TYPE 133 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     18   33
  17Q GAIN WILD-TYPE  133  211
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               18                133
  MALE                 33                211
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17Q GAIN MUTATED                                       5
  17Q GAIN WILD-TYPE                                    60
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                       20
  17Q GAIN WILD-TYPE                                                    137
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                                   9
  17Q GAIN WILD-TYPE                                                                60
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  17Q GAIN MUTATED                                                 11
  17Q GAIN WILD-TYPE                                               53
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17Q GAIN MUTATED                                                          2
  17Q GAIN WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  17Q GAIN MUTATED                                                           0
  17Q GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17Q GAIN MUTATED                                          3
  17Q GAIN WILD-TYPE                                        6
D31V8, multiclass
                                                                   clus
vv                                                                  17Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  17Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1  50
  17Q GAIN WILD-TYPE   5 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   50
  17Q GAIN WILD-TYPE    5  339
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 1                  5
  YES               50                339
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    42   0   6   1
  17Q GAIN WILD-TYPE 276  16  12  24
D31V10, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               42                276
  R1                0                 16
  R2                6                 12
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17Q GAIN MUTATED       8                         2
  17Q GAIN WILD-TYPE    80                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    32
  17Q GAIN WILD-TYPE                                         1   211
D31V12, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                                    8                 80
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   32                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"

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    38  32
  18P GAIN WILD-TYPE 204  90
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                70                294 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                32                 90 
$`18P GAIN MUTATED`
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6565 TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-8060 
        6.97        18.35         0.62         0.16         0.95         1.32 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.69         0.49         0.72         1.55         1.48         7.40 
TCGA-BR-8362 TCGA-BR-8370 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8687 
        0.36         3.32         9.21        20.22         1.12         0.62 
TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5798 TCGA-CD-5799 
        0.72        13.51        20.65         1.15         2.83         3.25 
TCGA-CD-5800 TCGA-CD-A486 TCGA-CD-A4MH TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5724 
       13.15         6.35         0.10        21.99        22.98        12.03 
TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8576 
       11.93        17.19         4.14        15.22        12.79         6.97 
TCGA-D7-A4YY TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-FP-8631 
       13.78        11.31         2.96        15.65         7.40         0.56 
TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF 
        1.55        26.47         5.92         0.76        22.75        25.81 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       12.30        27.42        18.38        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A663 TCGA-RD-A8N9 TCGA-VQ-A8DL 
        6.74         5.56        60.56         4.31        35.61         0.92 
TCGA-VQ-A8E3 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A91E 
       21.73         2.70        17.85         1.87         9.27         8.68 
TCGA-VQ-A91U TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-ZQ-A9CR 
        1.71         8.61        40.08         0.79 

$`18P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 
        5.62        11.70         6.61         4.64         7.43        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       10.13        13.68         7.00        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
       35.24        23.93        15.42        28.01         0.69        18.54 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       12.26        20.55         0.26        12.95         0.26        16.31 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       13.74         4.31        14.04         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         0.59        15.68 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 
        0.92        13.41        13.51        12.89         0.79        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        12.82         0.66        19.36         0.46        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
       13.64        11.57         5.13        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI 
        0.13         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        7.99         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        30.97         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       17.85         5.95        15.98        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19         0.23        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        15.16        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B 
       13.71        11.24        11.44         9.76         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        0.62         7.79        16.24         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27         8.12         0.39        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         0.23        18.08 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
        3.25        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       19.36        17.69         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RS 
        3.45        18.81         3.39         5.36         5.19         6.87 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        1.81         2.53         5.56        28.90         3.72        19.73 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW 
       11.05         8.61         4.67        16.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87         5.79        37.74         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       31.10        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
       46.26        16.31        23.41        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       64.57        14.33        59.18        28.70        11.70        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 
       20.81         7.36         8.58         9.73        44.25        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        4.54         6.58         5.72        29.98        21.11         4.21 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.10               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             60.56             122.30 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             6.855             12.315 
[1] "0.1 - 60.6 (6.9)"   "0.1 - 122.3 (12.3)"
[1] "hr=" "2"  
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         0        3        8        5         7         9
  18P GAIN WILD-TYPE       2       10       31       26        29        40
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           0         14          9         13        7
  18P GAIN WILD-TYPE         3         63         46         24       30
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 10
  STAGE IB                  8                 31
  STAGE II                  5                 26
  STAGE IIA                 7                 29
  STAGE IIB                 9                 40
  STAGE III                 0                  3
  STAGE IIIA               14                 63
  STAGE IIIB                9                 46
  STAGE IIIC               13                 24
  STAGE IV                  7                 30
[1] 11  2
[1] TRUE
[1] "dimension of 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     7  12  32  24
  18P GAIN WILD-TYPE  14  75 141  80
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                7                 14
  T2               12                 75
  T3               32                141
  T4               24                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18P GAIN MUTATED   24 19 13 20
  18P GAIN WILD-TYPE 98 88 62 59
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               24                 98
  N1               19                 88
  N2               13                 62
  N3               20                 59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  18P GAIN MUTATED    69   4   5
  18P GAIN WILD-TYPE 284  20  13
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               69                284
  M1                4                 20
  MX                5                 13
[1] 3 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    34  44
  18P GAIN WILD-TYPE 117 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     34   44
  18P GAIN WILD-TYPE  117  200
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               34                117
  MALE                 44                200
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18P GAIN MUTATED                                       6
  18P GAIN WILD-TYPE                                    59
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                       32
  18P GAIN WILD-TYPE                                                    125
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                                  11
  18P GAIN WILD-TYPE                                                                58
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  18P GAIN MUTATED                                                 17
  18P GAIN WILD-TYPE                                               47
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18P GAIN MUTATED                                                          4
  18P GAIN WILD-TYPE                                                       17
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  18P GAIN MUTATED                                                           3
  18P GAIN WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18P GAIN MUTATED                                          4
  18P GAIN WILD-TYPE                                        5
D32V8, multiclass
                                                                   clus
vv                                                                  18P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         4
                                                                   clus
vv                                                                  18P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4  74
  18P GAIN WILD-TYPE   2 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4   74
  18P GAIN WILD-TYPE    2  315
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 4                  2
  YES               74                315
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    61   5   4   4
  18P GAIN WILD-TYPE 257  11  14  21
D32V10, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               61                257
  R1                5                 11
  R2                4                 14
  RX                4                 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"
D32V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED      16                         0
  18P GAIN WILD-TYPE    72                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           0    51
  18P GAIN WILD-TYPE                                         1   192
D32V12, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                                   16                 72
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   51                192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    26  18
  18Q GAIN WILD-TYPE 216 104
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                44                320 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                18                104 
$`18Q GAIN MUTATED`
TCGA-BR-4184 TCGA-BR-6565 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8284 
        6.97         0.62         0.95         0.69         0.49         0.72 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8484 TCGA-BR-8487 
        1.55         1.48         7.40         0.36         0.72         1.12 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5798 
        0.92         0.72        13.51        20.65         1.15         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CG-4460 TCGA-D7-5579 TCGA-D7-6528 TCGA-D7-6817 
        3.25        13.15        21.99        11.93        15.22        12.79 
TCGA-D7-A4YY TCGA-D7-A6EX TCGA-FP-8631 TCGA-FP-A4BF TCGA-HJ-7597 TCGA-HU-8243 
       13.78        11.31         0.56         1.55        26.47         5.92 
TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI 
        0.76        22.75        25.81        12.30        27.42        18.38 
TCGA-IN-A6RN TCGA-RD-A8N9 TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A91E 
       13.08        35.61         2.70         1.87         9.27         8.68 
TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       40.08         0.79 

$`18Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.16        18.54        12.43         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8285 
       17.49         0.82         1.32        12.26        20.55         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 
       12.95         0.26        16.31         6.18        19.50         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8588 
       15.85         3.72         5.39         9.21        20.22        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       10.68        12.56         1.15         0.66         3.02        22.26 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
       12.82         0.66        19.36         0.46        20.42        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
       11.57         5.13        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         6.35 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       29.98        47.05        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
        7.07        12.00        22.98        30.97         6.97         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85         5.95        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
        4.14        15.98        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       16.80        19.50        17.19         0.23         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4Z0 
       20.91        14.27        16.44         5.92        15.16        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.24        11.44         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        6.58        14.47        72.23        21.27         8.12         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53         3.02        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 
       13.58         0.23        18.08         1.51        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        11.41        12.10        10.62        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GJ 
       12.30        11.84        24.20         3.25        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        17.69         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19         1.41         6.44         6.74         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        5.56         1.81         2.53         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
       37.74         5.46        13.25        13.02        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
       16.31        17.85        23.41        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
       64.57        14.33        59.18        28.70        11.70        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81         1.71         7.36         8.58         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B 
        8.61        55.43         4.54         6.58         5.72        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       21.11         4.21 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.36               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             40.08             122.30 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             6.445             12.015 
[1] "0.4 - 40.1 (6.4)"   "0.1 - 122.3 (12.0)"
[1] "hr=" "1.7"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         0        1        5        4         2         6
  18Q GAIN WILD-TYPE       2       12       34       27        34        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           0         10          5         11        5
  18Q GAIN WILD-TYPE         3         67         50         26       32
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 12
  STAGE IB                  5                 34
  STAGE II                  4                 27
  STAGE IIA                 2                 34
  STAGE IIB                 6                 43
  STAGE III                 0                  3
  STAGE IIIA               10                 67
  STAGE IIIB                5                 50
  STAGE IIIC               11                 26
  STAGE IV                  5                 32
[1] 11  2
[1] TRUE
[1] "dimension of 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     3   8  15  23
  18Q GAIN WILD-TYPE  18  79 158  81
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                3                 18
  T2                8                 79
  T3               15                158
  T4               23                 81
[1] 4 2
[1] TRUE
[1] "dimension of 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    15  10   9  15
  18Q GAIN WILD-TYPE 107  97  66  64
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               15                107
  N1               10                 97
  N2                9                 66
  N3               15                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  18Q GAIN MUTATED    43   3   5
  18Q GAIN WILD-TYPE 310  21  13
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0               43                310
  M1                3                 21
  MX                5                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    22  29
  18Q GAIN WILD-TYPE 129 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     22   29
  18Q GAIN WILD-TYPE  129  215
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               22                129
  MALE                 29                215
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18Q GAIN MUTATED                                       4
  18Q GAIN WILD-TYPE                                    61
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                       20
  18Q GAIN WILD-TYPE                                                    137
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                                   6
  18Q GAIN WILD-TYPE                                                                63
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  18Q GAIN MUTATED                                                 11
  18Q GAIN WILD-TYPE                                               53
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18Q GAIN MUTATED                                                          4
  18Q GAIN WILD-TYPE                                                       17
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  18Q GAIN MUTATED                                                           2
  18Q GAIN WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18Q GAIN MUTATED                                          4
  18Q GAIN WILD-TYPE                                        5
D33V8, multiclass
                                                                   clus
vv                                                                  18Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         4
                                                                   clus
vv                                                                  18Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     3  48
  18Q GAIN WILD-TYPE   3 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3   48
  18Q GAIN WILD-TYPE    3  341
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 3                  3
  YES               48                341
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    40   3   3   3
  18Q GAIN WILD-TYPE 278  13  15  22
D33V10, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               40                278
  R1                3                 13
  R2                3                 15
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18Q GAIN MUTATED      12                         0
  18Q GAIN WILD-TYPE    76                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           0    33
  18Q GAIN WILD-TYPE                                         1   210
D33V12, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                                   12                 76
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   33                210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    31   9
  19P GAIN WILD-TYPE 211 113
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                40                324 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 9                113 
$`19P GAIN MUTATED`
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8370 
       10.13         7.00        18.71        12.95        16.31         3.32 
TCGA-BR-A453 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8530 
        3.02        13.51        13.64        13.18         0.07         0.16 
TCGA-CD-8535 TCGA-CD-A48C TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4475 
        0.13         0.13        47.05        19.07        21.99        22.98 
TCGA-CG-5722 TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 
        0.99         4.01        12.36        19.13        20.55        18.54 
TCGA-D7-6528 TCGA-D7-8578 TCGA-D7-A4YU TCGA-EQ-A4SO TCGA-FP-A4BF TCGA-HU-8249 
       15.22        21.14        16.44        16.24         1.55        14.17 
TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD TCGA-HU-A4H2 TCGA-IN-7808 TCGA-IN-A6RP 
       12.10        24.30        22.75        12.95         3.45         6.44 
TCGA-SW-A7EB TCGA-VQ-A8E3 TCGA-VQ-A91A TCGA-VQ-A925 
        5.79        21.73        28.70         4.54 

$`19P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        13.12        13.68        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49         0.82         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
       20.55         0.72         0.26         0.26         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
        2.96         0.95        13.74         4.31        14.04         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39         0.72         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        12.56         1.15         0.66        22.26         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         0.79         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82         0.66        19.36         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 
       13.15         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 
        0.10         0.13         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH 
        6.35         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       29.98        12.03         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         1.02         0.99         6.02 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       55.04        21.07         7.99        12.66        11.93        18.84 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       18.61        17.85         5.95        17.19         4.14        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19         0.23         6.97        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 
       11.31        11.44         9.76         2.96        15.65         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 
        7.40         7.13         0.62         7.79         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27         8.12         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       22.29        17.06        59.54         5.03        13.58         0.56 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.23        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.59        11.41        10.62         0.76         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        19.36        17.69        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        27.42        21.21        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR 
       18.38         5.36         5.19        13.08         1.41         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.87         5.56         1.81         2.53         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT 
       28.90         3.72        19.73         4.31        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.67        16.67       122.30        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        37.74         5.46        13.25        13.02        31.10 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W 
       11.70         8.68        49.25        20.81         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
        8.58         9.73        44.25         8.61        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        40.08        29.98        21.11         4.21         0.79 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.07               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             47.05             122.30 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            13.345             11.310 
[1] "0.1 - 47.0 (13.3)"  "0.1 - 122.3 (11.3)"
[1] "hr=" "1.6"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         0        0        3        3         3         7
  19P GAIN WILD-TYPE       2       13       36       28        33        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           1         13          7          2        6
  19P GAIN WILD-TYPE         2         64         48         35       31
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 13
  STAGE IB                  3                 36
  STAGE II                  3                 28
  STAGE IIA                 3                 33
  STAGE IIB                 7                 42
  STAGE III                 1                  2
  STAGE IIIA               13                 64
  STAGE IIIB                7                 48
  STAGE IIIC                2                 35
  STAGE IV                  6                 31
[1] 11  2
[1] TRUE
[1] "dimension of 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     1  12  27   6
  19P GAIN WILD-TYPE  20  75 146  98
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                1                 20
  T2               12                 75
  T3               27                146
  T4                6                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19P GAIN MUTATED     8  18   8  12
  19P GAIN WILD-TYPE 114  89  67  67
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                8                114
  N1               18                 89
  N2                8                 67
  N3               12                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  19P GAIN MUTATED    40   6   2
  19P GAIN WILD-TYPE 313  18  16
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               40                313
  M1                6                 18
  MX                2                 16
[1] 3 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    20  28
  19P GAIN WILD-TYPE 131 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     20   28
  19P GAIN WILD-TYPE  131  216
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               20                131
  MALE                 28                216
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19P GAIN MUTATED                                      10
  19P GAIN WILD-TYPE                                    55
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                       17
  19P GAIN WILD-TYPE                                                    140
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                                   5
  19P GAIN WILD-TYPE                                                                64
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  19P GAIN MUTATED                                                  8
  19P GAIN WILD-TYPE                                               56
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19P GAIN MUTATED                                                          5
  19P GAIN WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  19P GAIN MUTATED                                                           0
  19P GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19P GAIN MUTATED                                          2
  19P GAIN WILD-TYPE                                        7
D34V8, multiclass
                                                                   clus
vv                                                                  19P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           10
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                5
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  19P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             55
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 64
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  56
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     2  46
  19P GAIN WILD-TYPE   4 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   46
  19P GAIN WILD-TYPE    4  343
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 2                  4
  YES               46                343
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    34   3   5   4
  19P GAIN WILD-TYPE 284  13  13  21
D34V10, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               34                284
  R1                3                 13
  R2                5                 13
  RX                4                 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"
D34V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED      11                         0
  19P GAIN WILD-TYPE    77                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           0    28
  19P GAIN WILD-TYPE                                         1   215
D34V12, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                                   11                 77
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   28                215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    41  16
  19Q GAIN WILD-TYPE 201 106
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                307 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                16                106 
$`19Q GAIN MUTATED`
TCGA-BR-6458 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8370 
        7.00        28.01        18.71        12.95        16.31         3.32 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8690 TCGA-BR-A453 TCGA-BR-A4J1 TCGA-BR-A4J8 
        9.21         1.12        10.68         3.02         0.72        13.51 
TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48C 
       13.18         0.07         0.07         0.16         0.13         0.13 
TCGA-CG-4438 TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5722 TCGA-CG-5730 
       54.08        47.05        21.99        22.98         0.99         4.01 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
       12.36        19.13        18.54        10.55        12.33        24.72 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-FP-7916 
       21.14        16.44         7.79        16.24        72.23         3.02 
TCGA-FP-A4BF TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4G2 TCGA-HU-A4GD 
        1.55        14.27        14.17        12.10        24.30        22.75 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-IN-7808 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A6F7 
        2.10        12.95         3.45         5.19         6.44        60.56 
TCGA-RD-A7BT TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8P5 
        8.61        35.61         5.79        13.25        21.73         7.73 
TCGA-VQ-A91A TCGA-VQ-A91U TCGA-VQ-A925 
       28.70         1.71         4.54 

$`19Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.12        10.13        13.68        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 
        9.21        24.76        35.24        23.93        15.42         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49         0.82         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
       20.55         0.72         0.26         0.26         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8371 
        2.96         0.95        13.74         4.31        14.04         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        5.39         0.72        20.22        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         0.59        15.68         0.62        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        0.66        22.26         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.13         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.07         0.10         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 
       27.02        15.95         1.02         7.99         8.05         4.01 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        19.07        12.03         9.01        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02       105.07        12.03        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 
       79.07        65.10        55.04        21.07         7.99        12.66 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       11.93        20.55        18.84        18.61        17.85         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6820 
       17.19         4.14        15.22        15.98        12.79        11.31 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8579 
       16.80        19.50        17.19         0.23         6.97        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        4.34         7.40         7.13         0.62         6.58        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 
       21.27         8.12         0.39        19.53        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03        13.58         0.56         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 
       26.47         1.51         5.92        12.59        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
        0.76         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
        6.51         6.25        10.19         0.26        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.30         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO 
       18.81         3.39        18.38         5.36        13.08         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
        6.74         6.87         5.56         1.81         2.53         5.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW 
       28.90         3.72        19.73         4.31        11.05         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       71.38        57.44         8.94        16.87         0.92        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 
        5.46        13.02        31.10        22.36        23.77        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       33.63        46.26        16.31         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        19.30        23.57        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       14.33        59.18        11.70         8.68        49.25        20.81 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         8.58         9.73        44.25         8.61        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        6.58         5.72        40.08        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.07               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             72.23             122.30 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             12.33              11.54 
[1] "0.1 - 72.2 (12.3)"  "0.1 - 122.3 (11.5)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         0        2        5        4         4         8
  19Q GAIN WILD-TYPE       2       11       34       27        32        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           1         18          8          5        8
  19Q GAIN WILD-TYPE         2         59         47         32       29
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 11
  STAGE IB                  5                 34
  STAGE II                  4                 27
  STAGE IIA                 4                 32
  STAGE IIB                 8                 41
  STAGE III                 1                  2
  STAGE IIIA               18                 59
  STAGE IIIB                8                 47
  STAGE IIIC                5                 32
  STAGE IV                  8                 29
[1] 11  2
[1] TRUE
[1] "dimension of 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     3  15  35  11
  19Q GAIN WILD-TYPE  18  72 138  93
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                3                 18
  T2               15                 72
  T3               35                138
  T4               11                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q GAIN MUTATED    13  23   9  19
  19Q GAIN WILD-TYPE 109  84  66  60
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               13                109
  N1               23                 84
  N2                9                 66
  N3               19                 60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  19Q GAIN MUTATED    56   6   4
  19Q GAIN WILD-TYPE 297  18  14
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               56                297
  M1                6                 18
  MX                4                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    25  41
  19Q GAIN WILD-TYPE 126 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     25   41
  19Q GAIN WILD-TYPE  126  203
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               25                126
  MALE                 41                203
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19Q GAIN MUTATED                                      13
  19Q GAIN WILD-TYPE                                    52
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                       23
  19Q GAIN WILD-TYPE                                                    134
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                                  13
  19Q GAIN WILD-TYPE                                                                56
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  19Q GAIN MUTATED                                                 10
  19Q GAIN WILD-TYPE                                               54
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19Q GAIN MUTATED                                                          4
  19Q GAIN WILD-TYPE                                                       17
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  19Q GAIN MUTATED                                                           0
  19Q GAIN WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19Q GAIN MUTATED                                          2
  19Q GAIN WILD-TYPE                                        7
D35V8, multiclass
                                                                   clus
vv                                                                  19Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  19Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     4  62
  19Q GAIN WILD-TYPE   2 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      4   62
  19Q GAIN WILD-TYPE    2  327
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 4                  2
  YES               62                327
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    48   4   6   4
  19Q GAIN WILD-TYPE 270  12  12  21
D35V10, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               48                270
  R1                4                 12
  R2                6                 12
  RX                4                 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"
D35V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19Q GAIN MUTATED      18                         1
  19Q GAIN WILD-TYPE    70                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           1    35
  19Q GAIN WILD-TYPE                                         0   208
D35V12, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                                   18                 70
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   35                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"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   137  65
  20P GAIN WILD-TYPE 105  57
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               202                162 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                65                 57 
$`20P GAIN MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4280 
        6.61         6.97         4.64        18.35        30.90         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 
       15.95        13.12        13.68         7.00        39.12         0.62 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       13.22        16.14        21.11        12.82         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 
       15.42         0.69         0.16        18.54         0.95        12.76 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8291 
       18.71         1.32         0.69         0.49         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 
        1.55         1.48         7.40        14.04        14.79         0.26 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 
        5.39         0.72         9.21        20.22        15.81         2.14 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        7.53         0.49        11.54         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       10.68         1.15         0.66        22.26         0.92         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
        0.53        13.51         0.46        20.42         1.15        13.64 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
        3.25        13.15        13.18         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.10         0.13         0.16         0.10         0.13 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        0.13         6.35         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
        0.10         0.10        20.02        27.02        15.95         7.99 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 
       54.08         4.01        14.01        47.05        12.03        18.97 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 
        7.07        12.00        30.97         1.02         1.02         0.99 
TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5734 TCGA-D7-5577 
       12.03        28.96        79.07         4.01         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       12.66        11.93        19.13        18.54         5.95        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
        4.14        15.22        10.55        11.31        12.33        24.72 
TCGA-D7-8573 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       19.50        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.24        11.31         9.76         2.96        15.65 
TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 
        7.40         7.79        14.47        72.23         8.12        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
        3.02        22.29        17.06         0.56         1.55         0.23 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8608 
       26.47         1.51         5.92        14.27        12.59        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
        0.76        24.30        12.30         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       11.77         8.98         0.10         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 
        2.10        12.95        17.69         9.67        27.42        21.21 
TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
        3.45        18.38         5.19         6.74         6.87         5.56 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT 
        1.81         5.56        60.56        28.90         4.31         8.61 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
       16.67       115.69        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC TCGA-VQ-A8PJ 
       13.25        13.02        31.10        21.73        46.26         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       17.85        15.65        23.57        64.57        59.18        28.70 
TCGA-VQ-A91E TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        8.68         1.71         7.36         9.73        44.25         8.61 
TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        29.98         4.21         0.79 

$`20P GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4188 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        5.62        11.70         7.43         6.18         9.57        34.68 
TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 
       10.13         0.82        32.78        13.84         1.25         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 
       30.90        31.20        32.94        24.76        23.93        28.01 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 
       12.43         0.69        17.49         0.82        12.26        20.55 
TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        0.72        12.95         0.26         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8382 TCGA-BR-8384 
        3.32         0.36        19.17         0.69        15.85         3.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8680 TCGA-BR-8682 
        1.12        12.79        13.45         0.20        15.81        16.44 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       12.56         3.02        13.41        13.51        12.89         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4QL 
       14.17        12.82         0.66        19.36        20.65        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8531 TCGA-CD-8536 
        5.13         2.83         0.30         0.07         0.10         0.10 
TCGA-CD-A489 TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4443 
        0.13         0.10         3.02         1.02         8.05        29.98 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5720 
       19.07        21.99         9.01        22.98         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
        6.02       105.07        15.02        65.10        55.04        21.07 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6815 TCGA-D7-6817 
       20.55        18.84        18.61        17.85        15.98        12.79 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YY 
       16.80        17.19         0.23         6.97        21.14        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO 
       14.76        11.44         4.34         7.13         0.62        16.24 
TCGA-F1-6177 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        6.58        21.27         0.39        59.54         5.03        13.58 
TCGA-HF-A5NB TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4G3 TCGA-HU-A4G8 
       18.08        14.17        11.41        12.10         5.59        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H5 
       24.20        21.37        29.98         6.51        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RN 
        8.88         8.81        18.81         3.39         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        1.41         6.44         2.53         3.72        19.73        11.05 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        4.67       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       16.87         0.92        37.74         5.46        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO 
        7.73        19.07        33.63        16.31         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q 
       23.41        19.30        14.33        11.70        49.25        20.81 
TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6J 
        8.58        55.43         4.54         6.58        40.08        21.11 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.07 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            115.69             122.30 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             9.975             12.675 
[1] "0.1 - 115.7 (10.0)" "0.1 - 122.3 (12.7)"
[1] "hr=" "1"  
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         1        9       18       16        19        25
  20P GAIN WILD-TYPE       1        4       21       15        17        24
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           2         50         28         20       17
  20P GAIN WILD-TYPE         1         27         27         17       20
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  9                  4
  STAGE IB                 18                 21
  STAGE II                 16                 15
  STAGE IIA                19                 17
  STAGE IIB                25                 24
  STAGE III                 2                  1
  STAGE IIIA               50                 27
  STAGE IIIB               28                 27
  STAGE IIIC               20                 17
  STAGE IV                 17                 20
[1] 11  2
[1] TRUE
[1] "dimension of 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    11  46 103  49
  20P GAIN WILD-TYPE  10  41  70  55
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               11                 10
  T2               46                 41
  T3              103                 70
  T4               49                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20P GAIN MUTATED   60 67 40 40
  20P GAIN WILD-TYPE 62 40 35 39
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               60                 62
  N1               67                 40
  N2               40                 35
  N3               40                 39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  20P GAIN MUTATED   193  11  11
  20P GAIN WILD-TYPE 160  13   7
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0              193                160
  M1               11                 13
  MX               11                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    71 144
  20P GAIN WILD-TYPE  80 100
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     71  144
  20P GAIN WILD-TYPE   80  100
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               71                 80
  MALE                144                100
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  20P GAIN MUTATED                                      27
  20P GAIN WILD-TYPE                                    38
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                       81
  20P GAIN WILD-TYPE                                                     76
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                                  45
  20P GAIN WILD-TYPE                                                                24
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  20P GAIN MUTATED                                                 40
  20P GAIN WILD-TYPE                                               24
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  20P GAIN MUTATED                                                         10
  20P GAIN WILD-TYPE                                                       11
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  20P GAIN MUTATED                                                           5
  20P GAIN WILD-TYPE                                                         3
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  20P GAIN MUTATED                                          6
  20P GAIN WILD-TYPE                                        3
D36V8, multiclass
                                                                   clus
vv                                                                  20P GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           27
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          81
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               45
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         6
                                                                   clus
vv                                                                  20P GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             38
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            76
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 24
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2 213
  20P GAIN WILD-TYPE   4 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  213
  20P GAIN WILD-TYPE    4  176
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 2                  4
  YES              213                176
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED   174   7   9  14
  20P GAIN WILD-TYPE 144   9   9  11
D36V10, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              174                144
  R1                7                  9
  R2                9                  9
  RX               14                 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"
D36V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20P GAIN MUTATED      53                         2
  20P GAIN WILD-TYPE    35                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           1   130
  20P GAIN WILD-TYPE                                         0   113
D36V12, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                                   53                 35
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  130                113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   155  77
  20Q GAIN WILD-TYPE  87  45
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               232                132 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                77                 45 
$`20Q GAIN MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4280 
        6.61         6.97         4.64        18.35        30.90         6.61 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6801 TCGA-BR-7196 
        0.82         0.62        13.22        16.14        21.11        12.82 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        35.24        15.42         0.69         0.16        18.54 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.95        12.76        18.71         0.82         1.32         0.69 
TCGA-BR-8080 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.49         0.26         0.26        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 TCGA-BR-8484 
        7.40        14.04        14.79         0.26         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8676 TCGA-BR-8677 
        9.21        20.22        15.81         2.14         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
       11.54        16.44         0.59        15.68         0.62        10.68 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 
        1.15         0.66        22.26         0.92        12.89         0.72 
TCGA-BR-A4J4 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.53        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 TCGA-CD-8525 
       13.64         3.25        13.15        13.18         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.13         6.35         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.07         0.10         0.10        20.02        27.02        15.95 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        7.99         8.05        54.08         4.01        14.01        47.05 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
       12.03        18.97         7.07        12.00        22.98        30.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        1.02         1.02         0.99        12.03        28.96        79.07 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        55.04         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 
       19.13        20.55        18.84        18.54         5.95        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14        15.22        15.98        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       24.72        16.80        19.50         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A6ET TCGA-D7-A6EV 
       14.27        16.44         5.92        15.16        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 
       11.31         9.76         2.96        15.65         7.40         7.79 
TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       16.24        14.47        72.23         8.12         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
        3.02        22.29        17.06         0.56         1.55         0.23 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GC 
       12.10        10.62         0.76        24.30        12.30         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       22.75        25.81        11.77         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI 
        9.67        27.42        21.21         3.45         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        5.19         6.74         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 
        5.56        60.56        28.90         4.31         8.61        16.67 
TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
       37.91       115.69        57.44         8.94        35.61         5.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8PC 
        5.46        13.25        13.02        31.10        21.73        46.26 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PQ TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
        2.70        17.85        15.65        23.57        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
       59.18        28.70         8.68         1.71         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-AA68 
        9.73        44.25         8.61         4.54         5.72        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        21.11         4.21         0.79 

$`20Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4188 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6452 
        5.62        11.70         7.43         6.18         9.57        34.68 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6803 
       32.78        13.84         1.25         8.98        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7851 TCGA-BR-7957 
       32.94        24.76        23.93        28.01        12.43         0.69 
TCGA-BR-8058 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8360 
       17.49        12.26        20.55         0.72        12.95         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 
       13.74         4.31         3.32         0.36        19.17         0.69 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8591 TCGA-BR-8592 
       15.85         3.72         1.12        12.79        13.45         0.20 
TCGA-BR-8680 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       15.81        12.56         3.02        13.41        13.51         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL TCGA-BR-A4QM 
       14.17        12.82         0.66        19.36        11.57         5.13 
TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A489 
        2.83         0.30         0.07         0.10         0.10         0.13 
TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 
        0.10         3.02         1.02        29.98        19.07        21.99 
TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5725 
        9.01         6.97         0.99         6.02       105.07        15.02 
TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-8574 
       65.10        21.07        18.61        17.85        12.79        17.19 
TCGA-D7-8575 TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B 
        0.23        13.78        14.76        11.44         4.34         7.13 
TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-A448 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        0.62         6.58        21.27        59.54         5.03        13.58 
TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ 
       18.08        11.41         5.59        11.84        24.20        21.37 
TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-8462 
       29.98         6.51        19.36         8.88         8.81        18.81 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.36        13.08         1.41         6.44         3.72        19.73 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05         4.67       122.30        40.64       116.38        71.38 
TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       16.87         0.92        37.74        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       19.07        33.63        16.31         1.87         9.27        23.41 
TCGA-VQ-A8PT TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A924 TCGA-VQ-A927 
       19.30        11.70        49.25        20.81        55.43         6.58 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            115.69             122.30 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            10.650             12.495 
[1] "0.1 - 115.7 (10.6)" "0.1 - 122.3 (12.5)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         1        9       22       17        21        33
  20Q GAIN WILD-TYPE       1        4       17       14        15        16
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           3         56         36         21       19
  20Q GAIN WILD-TYPE         0         21         19         16       18
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   1                  1
  STAGE IA                  9                  4
  STAGE IB                 22                 17
  STAGE II                 17                 14
  STAGE IIA                21                 15
  STAGE IIB                33                 16
  STAGE III                 3                  0
  STAGE IIIA               56                 21
  STAGE IIIB               36                 19
  STAGE IIIC               21                 16
  STAGE IV                 19                 18
[1] 11  2
[1] TRUE
[1] "dimension of 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    11  57 117  57
  20Q GAIN WILD-TYPE  10  30  56  47
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               11                 10
  T2               57                 30
  T3              117                 56
  T4               57                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20Q GAIN MUTATED   69 74 53 44
  20Q GAIN WILD-TYPE 53 33 22 35
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               69                 53
  N1               74                 33
  N2               53                 22
  N3               44                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  20Q GAIN MUTATED   221  12  15
  20Q GAIN WILD-TYPE 132  12   3
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0              221                132
  M1               12                 12
  MX               15                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    82 166
  20Q GAIN WILD-TYPE  69  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     82  166
  20Q GAIN WILD-TYPE   69   78
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               82                 69
  MALE                166                 78
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  20Q GAIN MUTATED                                      29
  20Q GAIN WILD-TYPE                                    36
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                       93
  20Q GAIN WILD-TYPE                                                     64
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                                  52
  20Q GAIN WILD-TYPE                                                                17
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  20Q GAIN MUTATED                                                 49
  20Q GAIN WILD-TYPE                                               15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  20Q GAIN MUTATED                                                         11
  20Q GAIN WILD-TYPE                                                       10
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  20Q GAIN MUTATED                                                           6
  20Q GAIN WILD-TYPE                                                         2
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  20Q GAIN MUTATED                                          6
  20Q GAIN WILD-TYPE                                        3
D37V8, multiclass
                                                                   clus
vv                                                                  20Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           29
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          93
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         6
                                                                   clus
vv                                                                  20Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             36
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            64
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     3 245
  20Q GAIN WILD-TYPE   3 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3  245
  20Q GAIN WILD-TYPE    3  144
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 3                  3
  YES              245                144
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   206   7  10  14
  20Q GAIN WILD-TYPE 112   9   8  11
D37V10, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              206                112
  R1                7                  9
  R2               10                  8
  RX               14                 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"
D37V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20Q GAIN MUTATED      59                         4
  20Q GAIN WILD-TYPE    29                         2
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           1   151
  20Q GAIN WILD-TYPE                                         0    92
D37V12, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                                   59                 29
  BLACK OR AFRICAN AMERICAN                                4                  2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  151                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    12   7
  21Q GAIN WILD-TYPE 230 115
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                19                345 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                115 
$`21Q GAIN MUTATED`
TCGA-BR-6456 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8486 
       10.13         0.95         0.69        12.95         1.55        20.22 
TCGA-BR-8687 TCGA-BR-A44U TCGA-CD-5799 TCGA-CD-A486 TCGA-D7-6527 TCGA-D7-6528 
        0.62         1.15         3.25         6.35         4.14        15.22 
TCGA-D7-6822 TCGA-D7-A6F0 TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4HD 
       12.33         2.96         5.92        22.75        11.77        27.42 
TCGA-IN-A6RP 
        6.44 

$`21Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.12        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 
        0.69         0.16        18.54        12.43         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 
       18.71        17.49         0.82         1.32        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
       20.55         0.72         0.26         0.26        16.31         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         0.72         9.21         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 
       11.54        15.81        16.44         0.59        15.68        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
       12.56         0.66         3.02        22.26         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         0.79         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.82         0.66        19.36        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03        21.99         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85         5.95        17.19 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        10.55        11.31        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19         0.23         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 
       13.71        11.24        11.31        11.44         9.76        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        6.58        14.47        72.23        21.27         8.12         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53         3.02        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         0.56         1.55         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        17.69        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        8.81        21.21         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19        13.08         1.41         6.74         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        5.56         1.81         2.53         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        37.74         5.46        13.25        13.02        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        19.30        23.57        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       59.18        28.70        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
        1.71         7.36         8.58         9.73        44.25         8.61 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B 
       55.43         4.54         6.58         5.72        40.08        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11         4.21         0.79 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.62               0.07 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             27.42             122.30 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              6.35              11.84 
[1] "0.6 - 27.4 (6.3)"   "0.1 - 122.3 (11.8)"
[1] "hr=" "1.5"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         0        2        3        3         2         4
  21Q GAIN WILD-TYPE       2       11       36       28        34        45
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           0          1          2          3        1
  21Q GAIN WILD-TYPE         3         76         53         34       36
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 11
  STAGE IB                  3                 36
  STAGE II                  3                 28
  STAGE IIA                 2                 34
  STAGE IIB                 4                 45
  STAGE III                 0                  3
  STAGE IIIA                1                 76
  STAGE IIIB                2                 53
  STAGE IIIC                3                 34
  STAGE IV                  1                 36
[1] 11  2
[1] TRUE
[1] "dimension of 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     3   5   8   5
  21Q GAIN WILD-TYPE  18  82 165  99
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                 18
  T2                5                 82
  T3                8                165
  T4                5                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q GAIN MUTATED     9   6   3   3
  21Q GAIN WILD-TYPE 113 101  72  76
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                9                113
  N1                6                101
  N2                3                 72
  N3                3                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  21Q GAIN MUTATED    20   1   0
  21Q GAIN WILD-TYPE 333  23  18
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0               20                333
  M1                1                 23
  MX                0                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     8  13
  21Q GAIN WILD-TYPE 143 231
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8   13
  21Q GAIN WILD-TYPE  143  231
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                8                143
  MALE                 13                231
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  21Q GAIN MUTATED                                       1
  21Q GAIN WILD-TYPE                                    64
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                       10
  21Q GAIN WILD-TYPE                                                    147
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                                   3
  21Q GAIN WILD-TYPE                                                                66
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  21Q GAIN MUTATED                                                  6
  21Q GAIN WILD-TYPE                                               58
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  21Q GAIN MUTATED                                                          0
  21Q GAIN WILD-TYPE                                                       21
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  21Q GAIN MUTATED                                                           1
  21Q GAIN WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  21Q GAIN MUTATED                                          0
  21Q GAIN WILD-TYPE                                        9
D38V8, multiclass
                                                                   clus
vv                                                                  21Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            1
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  21Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             64
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           147
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  21
  21Q GAIN WILD-TYPE   6 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   21
  21Q GAIN WILD-TYPE    6  368
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                  6
  YES               21                368
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    17   1   1   0
  21Q GAIN WILD-TYPE 301  15  17  25
D38V10, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               17                301
  R1                1                 15
  R2                1                 17
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  21Q GAIN MUTATED       6                         0
  21Q GAIN WILD-TYPE    82                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           0    14
  21Q GAIN WILD-TYPE                                         1   229
D38V12, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                                    6                 82
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   14                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"

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    20  10
  22Q GAIN WILD-TYPE 222 112
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                30                334 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                10                112 
$`22Q GAIN MUTATED`
TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8486 
       11.70         4.64        35.24        18.54        18.71        20.22 
TCGA-BR-A452 TCGA-BR-A4J8 TCGA-CD-5799 TCGA-CD-8525 TCGA-CD-8528 TCGA-CG-4436 
        0.66        13.51         3.25         0.07         0.10         7.99 
TCGA-D7-6521 TCGA-D7-6815 TCGA-D7-8576 TCGA-D7-A4Z0 TCGA-D7-A6F0 TCGA-F1-6875 
       18.54        15.98         6.97        14.76         2.96        72.23 
TCGA-FP-7998 TCGA-HU-8604 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H5 TCGA-IN-7808 
       22.29        12.10        11.77         6.25        12.30         3.45 
TCGA-IN-A6RO TCGA-KB-A6F7 TCGA-RD-A8N6 TCGA-VQ-A8PJ TCGA-VQ-A91D TCGA-VQ-AA68 
        1.41        60.56         8.94         2.70        11.70        40.08 

$`22Q GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62         6.61         6.97         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       10.13        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.95         0.69        12.76        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        1.32         0.69        12.26         0.49        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.26        12.95         0.26        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         0.72         9.21         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS 
       10.68        12.56         1.15         3.02        22.26         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         0.79         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82         0.66        19.36         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         9.01        18.97         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 
       12.66        11.93        19.13        20.55        18.84        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       17.85         5.95        17.19         4.14        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19         0.23        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
        5.92        15.16        13.78        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76        15.65         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        0.62         7.79        16.24         6.58        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8209 
        8.12         0.39        19.53         3.02        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         1.55         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       26.47         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        12.95        19.36        17.69         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        8.81        27.42        21.21        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19        13.08         6.44         6.74         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG 
        5.56         1.81         2.53         5.56        28.90         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       19.73         4.31        11.05         8.61         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       57.44        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        5.46        13.25        13.02        31.10        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       23.77         7.73        19.07        33.63        46.26        16.31 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91E 
       23.57        64.57        14.33        59.18        28.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       49.25        20.81         1.71         7.36         8.58         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
       44.25         8.61        55.43         4.54         6.58         5.72 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        21.11         4.21         0.79 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             72.23             122.30 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            11.735             11.490 
[1] "0.1 - 72.2 (11.7)"  "0.1 - 122.3 (11.5)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         0        4        5        2         2         3
  22Q GAIN WILD-TYPE       2        9       34       29        34        46
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           1          6          3          3        1
  22Q GAIN WILD-TYPE         2         71         52         34       36
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  4                  9
  STAGE IB                  5                 34
  STAGE II                  2                 29
  STAGE IIA                 2                 34
  STAGE IIB                 3                 46
  STAGE III                 1                  2
  STAGE IIIA                6                 71
  STAGE IIIB                3                 52
  STAGE IIIC                3                 34
  STAGE IV                  1                 36
[1] 11  2
[1] TRUE
[1] "dimension of 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     4  10   9   7
  22Q GAIN WILD-TYPE  17  77 164  97
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                4                 17
  T2               10                 77
  T3                9                164
  T4                7                 97
[1] 4 2
[1] TRUE
[1] "dimension of 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    12   6   6   6
  22Q GAIN WILD-TYPE 110 101  69  73
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               12                110
  N1                6                101
  N2                6                 69
  N3                6                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  22Q GAIN MUTATED    28   2   1
  22Q GAIN WILD-TYPE 325  22  17
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               28                325
  M1                2                 22
  MX                1                 17
[1] 3 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    13  18
  22Q GAIN WILD-TYPE 138 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     13   18
  22Q GAIN WILD-TYPE  138  226
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               13                138
  MALE                 18                226
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  22Q GAIN MUTATED                                       5
  22Q GAIN WILD-TYPE                                    60
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                        8
  22Q GAIN WILD-TYPE                                                    149
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                                   7
  22Q GAIN WILD-TYPE                                                                62
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  22Q GAIN MUTATED                                                  7
  22Q GAIN WILD-TYPE                                               57
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  22Q GAIN MUTATED                                                          3
  22Q GAIN WILD-TYPE                                                       18
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  22Q GAIN MUTATED                                                           1
  22Q GAIN WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  22Q GAIN MUTATED                                          0
  22Q GAIN WILD-TYPE                                        9
D39V8, multiclass
                                                                   clus
vv                                                                  22Q GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            5
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  22Q GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             60
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           149
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  31
  22Q GAIN WILD-TYPE   6 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   31
  22Q GAIN WILD-TYPE    6  358
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                  6
  YES               31                358
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    27   0   1   1
  22Q GAIN WILD-TYPE 291  16  17  24
D39V10, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               27                291
  R1                0                 16
  R2                1                 17
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  22Q GAIN MUTATED       9                         1
  22Q GAIN WILD-TYPE    79                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    18
  22Q GAIN WILD-TYPE                                         1   225
D39V12, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                                    9                 79
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   18                225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    27  20
  XQ GAIN WILD-TYPE 215 102
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               47               317 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               20               102 
$`XQ GAIN MUTATED`
TCGA-BR-4187 TCGA-BR-6458 TCGA-BR-6801 TCGA-BR-7717 TCGA-BR-8058 TCGA-BR-8059 
        4.64         7.00        21.11         0.69        17.49         0.82 
TCGA-BR-8077 TCGA-BR-8365 TCGA-BR-8683 TCGA-BR-A452 TCGA-CD-8528 TCGA-CD-A487 
        0.69         2.96         0.59         0.66         0.10         0.13 
TCGA-CD-A4MG TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4460 TCGA-CG-4472 TCGA-CG-5718 
        0.07         3.02         7.99        21.99        12.00         1.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8576 
       28.96        79.07        17.19        15.22        15.98         6.97 
TCGA-D7-A6EV TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 
       11.24         2.96        15.65         0.62         7.79        72.23 
TCGA-FP-7735 TCGA-HU-8244 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD 
        0.39        14.27        24.30        12.30        24.20        22.75 
TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4HD TCGA-RD-A8N6 TCGA-VQ-A8DT TCGA-VQ-A8PC 
       25.81         6.51        27.42         8.94        37.74        46.26 
TCGA-VQ-A8PY TCGA-VQ-A91E TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Z 
       14.33         8.68        20.81         1.71        44.25 

$`XQ GAIN WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.61         6.97         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.12        10.13        13.68        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7723 
       35.24        23.93        15.42        28.01         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 
       12.43         0.95         0.69        12.76        18.71         1.32 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         0.49        20.55         0.72         0.26        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.26        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.36         0.26        22.19         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44        15.68         0.62        10.68        12.56         1.15 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        3.02        22.26         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10         0.10        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 
        1.02         8.05        54.08         4.01        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        12.03         9.01        18.97         7.07 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        5.95         4.14        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19         0.23        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 
       14.76        13.71        11.31        11.44         9.76         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        7.40         7.13        16.24         6.58        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        8.12        19.53         3.02        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         1.55         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51         5.92        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC 
       12.10        10.62         0.76         5.59        11.84         3.25 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GU 
       11.77        21.37        29.98         8.98         0.10         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.30         9.67         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        1.41         6.44         6.74         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.31        11.05         8.61         4.67        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61        16.87         5.79         0.92         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.02        31.10        21.73        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       19.07        33.63        16.31         2.70        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX 
        9.27        23.41        15.65        19.30        23.57        64.57 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A91X 
       59.18        28.70        11.70        49.25         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73         8.61        55.43         4.54         6.58         5.72 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08        29.98        21.11         4.21         0.79 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.07              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            79.07            122.30 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            11.24             11.70 
[1] "0.1 - 79.1 (11.2)"  "0.1 - 122.3 (11.7)"
[1] "hr=" "1.3"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         1        5        6        2         5         7
  XQ GAIN WILD-TYPE       1        8       33       29        31        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           1          7          8          0        7
  XQ GAIN WILD-TYPE         2         70         47         37       30
D40V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 5                 8
  STAGE IB                 6                33
  STAGE II                 2                29
  STAGE IIA                5                31
  STAGE IIB                7                42
  STAGE III                1                 2
  STAGE IIIA               7                70
  STAGE IIIB               8                47
  STAGE IIIC               0                37
  STAGE IV                 7                30
[1] 11  2
[1] TRUE
[1] "dimension of 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     5  12  20  13
  XQ GAIN WILD-TYPE  16  75 153  91
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               5                16
  T2              12                75
  T3              20               153
  T4              13                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ GAIN MUTATED    20  16   9   4
  XQ GAIN WILD-TYPE 102  91  66  75
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              20               102
  N1              16                91
  N2               9                66
  N3               4                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  XQ GAIN MUTATED    46   3   2
  XQ GAIN WILD-TYPE 307  21  16
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              46               307
  M1               3                21
  MX               2                16
[1] 3 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    27  24
  XQ GAIN WILD-TYPE 124 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     27   24
  XQ GAIN WILD-TYPE  124  220
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              27               124
  MALE                24               220
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  XQ GAIN MUTATED                                       3
  XQ GAIN WILD-TYPE                                    62
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                       15
  XQ GAIN WILD-TYPE                                                    142
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                                  13
  XQ GAIN WILD-TYPE                                                                56
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  XQ GAIN MUTATED                                                 17
  XQ GAIN WILD-TYPE                                               47
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  XQ GAIN MUTATED                                                          0
  XQ GAIN WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  XQ GAIN MUTATED                                                           1
  XQ GAIN WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  XQ GAIN MUTATED                                          1
  XQ GAIN WILD-TYPE                                        8
D40V8, multiclass
                                                                   clus
vv                                                                  XQ GAIN MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         15
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              13
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  XQ GAIN WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          142
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                56
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  51
  XQ GAIN WILD-TYPE   6 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   51
  XQ GAIN WILD-TYPE    6  338
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                0                 6
  YES              51               338
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    42   0   3   3
  XQ GAIN WILD-TYPE 276  16  15  22
D40V10, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              42               276
  R1               0                16
  R2               3                15
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XQ GAIN MUTATED      14                         2
  XQ GAIN WILD-TYPE    74                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           0    25
  XQ GAIN WILD-TYPE                                         1   218
D40V12, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                                  14                74
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  25               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    32  18
  1P LOSS WILD-TYPE 210 104
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               50               314 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               18               104 
$`1P LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-7959 TCGA-BR-8289 
        6.61        10.13         7.00        35.24        18.71         0.26 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-A452 TCGA-BR-A4PD TCGA-BR-A4PE 
        9.21        11.54         0.59         0.66        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8533 
        1.15        13.64         3.25         0.30         0.07         0.13 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-5719 
        6.35         0.13        20.02         3.02        54.08         1.02 
TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 
       12.03         4.01        11.93        20.55        17.19         4.14 
TCGA-D7-6528 TCGA-D7-8573 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-HU-8249 
       15.22        19.50         7.40         0.62        16.24        14.17 
TCGA-HU-8604 TCGA-HU-A4HD TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-VQ-A8DV 
       12.10        27.42        28.90         4.31         8.61        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A91A TCGA-VQ-A91Z TCGA-VQ-A925 
       13.02         7.73         2.70        28.70        44.25         4.54 
TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       29.98         0.79 

$`1P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.12        13.68        39.12         0.82         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.95         0.69        12.76        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        1.32         0.69        12.26         0.49        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.26        12.95        16.31         1.55         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39         0.72        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        2.14        13.45         0.20         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44        15.68         0.62        10.68        12.56         1.15 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        3.02        22.26         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       19.36        13.51         0.46        11.57         5.13         2.83 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.18         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.10         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
        0.10         0.10        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        15.02        28.96        79.07        65.10 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       55.04        21.07         7.99        12.36        12.66        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 
       18.84        18.54        18.61        17.85         5.95        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19         0.23         6.97        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13         7.79         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27         8.12         0.39        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         1.55 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.23        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       12.59        11.41        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       17.69        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
        3.45        18.81         3.39        18.38         5.36         5.19 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
       13.08         1.41         6.44         6.74         6.87         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
        1.81         2.53         5.56        60.56         3.72        19.73 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         4.67        16.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 
       16.87         5.79         0.92        37.74         5.46        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       21.73        22.36        23.77        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       19.30        23.57        64.57        14.33        59.18        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
        8.68        49.25        20.81         1.71         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
        9.73         8.61        55.43         6.58         5.72        40.08 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       21.11         4.21 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            54.08            122.30 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            9.670            11.735 
[1] "0.1 - 54.1 (9.7)"   "0.1 - 122.3 (11.7)"
[1] "hr=" "1.2"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         0        0        4        6         7         4
  1P LOSS WILD-TYPE       2       13       35       25        29        45
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           0         10          7          2       10
  1P LOSS WILD-TYPE         3         67         48         35       27
D41V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                13
  STAGE IB                 4                35
  STAGE II                 6                25
  STAGE IIA                7                29
  STAGE IIB                4                45
  STAGE III                0                 3
  STAGE IIIA              10                67
  STAGE IIIB               7                48
  STAGE IIIC               2                35
  STAGE IV                10                27
[1] 11  2
[1] TRUE
[1] "dimension of 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     0  10  26  15
  1P LOSS WILD-TYPE  21  77 147  89
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               0                21
  T2              10                77
  T3              26               147
  T4              15                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P LOSS MUTATED    16  14  12   8
  1P LOSS WILD-TYPE 106  93  63  71
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              16               106
  N1              14                93
  N2              12                63
  N3               8                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  1P LOSS MUTATED    41   8   2
  1P LOSS WILD-TYPE 312  16  16
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              41               312
  M1               8                16
  MX               2                16
[1] 3 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    21  30
  1P LOSS WILD-TYPE 130 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     21   30
  1P LOSS WILD-TYPE  130  214
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              21               130
  MALE                30               214
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1P LOSS MUTATED                                       3
  1P LOSS WILD-TYPE                                    62
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                       17
  1P LOSS WILD-TYPE                                                    140
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                                  11
  1P LOSS WILD-TYPE                                                                58
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  1P LOSS MUTATED                                                 15
  1P LOSS WILD-TYPE                                               49
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  1P LOSS MUTATED                                                          3
  1P LOSS WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  1P LOSS MUTATED                                                           1
  1P LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  1P LOSS MUTATED                                          1
  1P LOSS WILD-TYPE                                        8
D41V8, multiclass
                                                                   clus
vv                                                                  1P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         17
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  1P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          140
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  51
  1P LOSS WILD-TYPE   6 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   51
  1P LOSS WILD-TYPE    6  338
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                0                 6
  YES              51               338
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    36   1   8   2
  1P LOSS WILD-TYPE 282  15  10  23
D41V10, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              36               282
  R1               1                15
  R2               8                10
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1P LOSS MUTATED      12                         1
  1P LOSS WILD-TYPE    76                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           1    30
  1P LOSS WILD-TYPE                                         0   213
D41V12, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                                  12                76
  BLACK OR AFRICAN AMERICAN                               1                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  30               213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    15  10
  1Q LOSS WILD-TYPE 227 112
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               339 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               112 
$`1Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-7704 TCGA-BR-8289 TCGA-BR-A4PD 
        6.61        10.13         7.00        35.24         0.26        20.65 
TCGA-CD-5799 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CG-5724 TCGA-CG-5730 
        3.25         6.35         0.13         0.13        12.03         4.01 
TCGA-D7-6519 TCGA-D7-A74A TCGA-EQ-A4SO TCGA-HU-8604 TCGA-HU-A4HD TCGA-IN-8663 
       20.55         7.40        16.24        12.10        27.42         3.39 
TCGA-IP-7968 TCGA-KB-A93H TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A925 TCGA-VQ-AA6B 
        2.53        28.90        13.25        13.02         4.54        29.98 
TCGA-ZQ-A9CR 
        0.79 

$`1Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.12        13.68        39.12         0.82         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         0.95         0.69        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.72         0.26        12.95        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39         0.72         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        0.49        11.54        15.81        16.44         0.59        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        0.62        10.68        12.56         1.15         0.66         3.02 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         0.92        13.41        13.51        12.89         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       13.51         0.46        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83        13.15        13.18         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03        21.99         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       79.07        65.10        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        11.93        19.13        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85         5.95        17.19         4.14        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19         0.23         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6177 
       15.65         4.34         7.13         0.62         7.79         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
       14.47        72.23        21.27         8.12         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        3.02        22.29        17.06        59.54         5.03        13.58 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        0.56         1.55         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 
        5.92        14.27        12.59        14.17        11.41        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        17.69        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI 
        8.88         8.81        21.21         3.45        18.81        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
        5.36         5.19        13.08         1.41         6.44         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
        6.87         5.56         1.81         5.56        60.56         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       19.73         4.31        11.05         8.61         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       37.74         5.46        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ 
        7.73        19.07        33.63        46.26        16.31         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       23.57        64.57        14.33        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
        8.68        49.25        20.81         1.71         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73        44.25         8.61        55.43         6.58         5.72 
TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 
       40.08        21.11         4.21 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.13              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            35.24            122.30 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              7.4              11.7 
[1] "0.1 - 35.2 (7.4)"   "0.1 - 122.3 (11.7)"
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         0        0        1        2         4         5
  1Q LOSS WILD-TYPE       2       13       38       29        32        44
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           0          5          3          1        4
  1Q LOSS WILD-TYPE         3         72         52         36       33
D42V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                13
  STAGE IB                 1                38
  STAGE II                 2                29
  STAGE IIA                4                32
  STAGE IIB                5                44
  STAGE III                0                 3
  STAGE IIIA               5                72
  STAGE IIIB               3                52
  STAGE IIIC               1                36
  STAGE IV                 4                33
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   5  15   5
  1Q LOSS WILD-TYPE  21  82 158  99
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               0                21
  T2               5                82
  T3              15               158
  T4               5                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q LOSS MUTATED     7   8   6   4
  1Q LOSS WILD-TYPE 115  99  69  75
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               7               115
  N1               8                99
  N2               6                69
  N3               4                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  1Q LOSS MUTATED    18   4   3
  1Q LOSS WILD-TYPE 335  20  15
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0              18               335
  M1               4                20
  MX               3                15
[1] 3 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    11  14
  1Q LOSS WILD-TYPE 140 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11   14
  1Q LOSS WILD-TYPE  140  230
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11               140
  MALE                14               230
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  1Q LOSS MUTATED                                       3
  1Q LOSS WILD-TYPE                                    62
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                        9
  1Q LOSS WILD-TYPE                                                    148
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                                   6
  1Q LOSS WILD-TYPE                                                                63
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  1Q LOSS MUTATED                                                  6
  1Q LOSS WILD-TYPE                                               58
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  1Q LOSS MUTATED                                                          0
  1Q LOSS WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  1Q LOSS MUTATED                                                           0
  1Q LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  1Q LOSS MUTATED                                          1
  1Q LOSS WILD-TYPE                                        8
D42V8, multiclass
                                                                   clus
vv                                                                  1Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  1Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          148
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0  25
  1Q LOSS WILD-TYPE   6 364
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0   25
  1Q LOSS WILD-TYPE    6  364
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                0                 6
  YES              25               364
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    16   0   4   1
  1Q LOSS WILD-TYPE 302  16  14  24
D42V10, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              16               302
  R1               0                16
  R2               4                14
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  1Q LOSS MUTATED       7                         1
  1Q LOSS WILD-TYPE    81                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0    15
  1Q LOSS WILD-TYPE                                         1   228
D42V12, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                                   7                81
  BLACK OR AFRICAN AMERICAN                               1                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  15               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"

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    12   9
  2P LOSS WILD-TYPE 230 113
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               21               343 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                9               113 
$`2P LOSS MUTATED`
TCGA-BR-6565 TCGA-BR-8060 TCGA-BR-8687 TCGA-CD-8535 TCGA-CD-A48A TCGA-CG-4475 
        0.62         1.32         0.62         0.13         0.13        22.98 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 TCGA-HJ-7597 
       12.66        11.93        17.19        15.22         6.97        26.47 
TCGA-HU-8243 TCGA-HU-A4GU TCGA-IN-A6RL TCGA-RD-A7C1 TCGA-RD-A8N9 TCGA-VQ-A8DU 
        5.92         6.25         5.19        16.67        35.61         5.46 
TCGA-VQ-A8PJ TCGA-VQ-A8PU TCGA-VQ-A91Z 
        2.70        23.57        44.25 

$`2P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.82        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49         0.82         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49        20.55         0.72         0.26        12.95         0.26 
TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       16.31         1.55         1.48         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         0.59        15.68        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         0.79         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       54.08         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99        12.36 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       19.13        20.55        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        5.95         4.14        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19         0.23 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX 
       21.14        20.91        14.27        16.44         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY 
       13.78        14.76        13.71        11.24        11.31        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
        9.76         2.96        15.65         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        0.62         7.79        16.24         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27         8.12         0.39        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         1.55 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
        0.23        18.08         1.51        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.30         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        1.41         6.44         6.74         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        4.31        11.05         8.61         4.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       16.87         5.79         0.92        37.74        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       31.10        21.73        22.36        23.77         7.73        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       33.63        46.26        16.31        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        19.30        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       28.70        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36         8.58         9.73         8.61        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        6.58         5.72        40.08        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.13              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            44.25            122.30 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             6.97             11.70 
[1] "0.1 - 44.2 (7.0)"   "0.1 - 122.3 (11.7)"
[1] "hr=" "1.5"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        0        4        2         1         4
  2P LOSS WILD-TYPE       2       13       35       29        35        45
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           0          7          2          3        2
  2P LOSS WILD-TYPE         3         70         53         34       35
D43V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                13
  STAGE IB                 4                35
  STAGE II                 2                29
  STAGE IIA                1                35
  STAGE IIB                4                45
  STAGE III                0                 3
  STAGE IIIA               7                70
  STAGE IIIB               2                53
  STAGE IIIC               3                34
  STAGE IV                 2                35
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   8  11   6
  2P LOSS WILD-TYPE  21  79 162  98
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                21
  T2               8                79
  T3              11               162
  T4               6                98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P LOSS MUTATED     7   7   7   4
  2P LOSS WILD-TYPE 115 100  68  75
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               7               115
  N1               7               100
  N2               7                68
  N3               4                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  2P LOSS MUTATED    22   1   2
  2P LOSS WILD-TYPE 331  23  16
D43V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0              22               331
  M1               1                23
  MX               2                16
[1] 3 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    12  13
  2P LOSS WILD-TYPE 139 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     12   13
  2P LOSS WILD-TYPE  139  231
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              12               139
  MALE                13               231
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  2P LOSS MUTATED                                       4
  2P LOSS WILD-TYPE                                    61
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                        8
  2P LOSS WILD-TYPE                                                    149
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                                   0
  2P LOSS WILD-TYPE                                                                69
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  2P LOSS MUTATED                                                  9
  2P LOSS WILD-TYPE                                               55
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  2P LOSS MUTATED                                                          2
  2P LOSS WILD-TYPE                                                       19
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  2P LOSS MUTATED                                                           0
  2P LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  2P LOSS MUTATED                                          1
  2P LOSS WILD-TYPE                                        8
D43V8, multiclass
                                                                   clus
vv                                                                  2P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          8
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  2P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          149
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2  23
  2P LOSS WILD-TYPE   4 366
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   23
  2P LOSS WILD-TYPE    4  366
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                2                 4
  YES              23               366
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    20   3   1   0
  2P LOSS WILD-TYPE 298  13  17  25
D43V10, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              20               298
  R1               3                13
  R2               1                17
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED       6                         0
  2P LOSS WILD-TYPE    82                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           0    15
  2P LOSS WILD-TYPE                                         1   228
D43V12, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                                   6                82
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  15               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"

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    15  10
  2Q LOSS WILD-TYPE 227 112
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               25               339 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               112 
$`2Q LOSS MUTATED`
TCGA-BR-6565 TCGA-BR-8687 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4300 
        0.62         0.62         0.13         6.35         0.13        20.02 
TCGA-CG-4475 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-8576 
       22.98        12.66        11.93        17.19        15.22         6.97 
TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4HD TCGA-IN-A6RL 
       26.47         5.92        22.75         6.25        27.42         5.19 
TCGA-IN-A6RO TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8PJ TCGA-VQ-A8PU 
        1.41        35.61         5.46        13.02         2.70        23.57 
TCGA-VQ-AA68 
       40.08 

$`2Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.82        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
        9.21        24.76        35.24        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
        0.69         0.16        18.54        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         0.49        20.55         0.72         0.26        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.26        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       14.79         0.69         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.72         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
       15.81        16.44         0.59        15.68        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
        1.15         0.66         3.02        22.26         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         0.79         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.82         0.66        19.36        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.10         0.13         0.10         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        0.13         0.07         0.10         0.10         0.10         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 
       21.99         9.01        18.97         7.07        12.00        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 
        4.01        55.04        21.07         7.99        12.36        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85         5.95 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19         0.23        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        2.96        15.65         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.79        16.24         6.58        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
        8.12         0.39        19.53         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX 
       59.54         5.03        13.58         0.56         1.55         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       18.08         1.51        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        17.69        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38         5.36        13.08         6.44         6.74         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        5.56         1.81         2.53         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       37.74        13.25        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK 
        7.73        19.07        33.63        46.26        16.31        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX 
        1.87         9.27        23.41        15.65        19.30        64.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        59.18        28.70        11.70         8.68        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
       20.81         1.71         7.36         8.58         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B 
        8.61        55.43         4.54         6.58         5.72        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11         4.21         0.79 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.13              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            40.08            122.30 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            11.93             11.57 
[1] "0.1 - 40.1 (11.9)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.3"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         0        1        3        2         2         4
  2Q LOSS WILD-TYPE       2       12       36       29        34        45
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           0          7          3          4        3
  2Q LOSS WILD-TYPE         3         70         52         33       34
D44V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                12
  STAGE IB                 3                36
  STAGE II                 2                29
  STAGE IIA                2                34
  STAGE IIB                4                45
  STAGE III                0                 3
  STAGE IIIA               7                70
  STAGE IIIB               3                52
  STAGE IIIC               4                33
  STAGE IV                 3                34
[1] 11  2
[1] TRUE
[1] "dimension of 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     1   6  14   8
  2Q LOSS WILD-TYPE  20  81 159  96
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               1                20
  T2               6                81
  T3              14               159
  T4               8                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q LOSS MUTATED     8   7   8   6
  2Q LOSS WILD-TYPE 114 100  67  73
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               8               114
  N1               7               100
  N2               8                67
  N3               6                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  2Q LOSS MUTATED    25   2   2
  2Q LOSS WILD-TYPE 328  22  16
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0              25               328
  M1               2                22
  MX               2                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    10  19
  2Q LOSS WILD-TYPE 141 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     10   19
  2Q LOSS WILD-TYPE  141  225
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              10               141
  MALE                19               225
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  2Q LOSS MUTATED                                       4
  2Q LOSS WILD-TYPE                                    61
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                        9
  2Q LOSS WILD-TYPE                                                    148
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                                   0
  2Q LOSS WILD-TYPE                                                                69
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  2Q LOSS MUTATED                                                 11
  2Q LOSS WILD-TYPE                                               53
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  2Q LOSS MUTATED                                                          2
  2Q LOSS WILD-TYPE                                                       19
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  2Q LOSS MUTATED                                                           0
  2Q LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  2Q LOSS MUTATED                                          2
  2Q LOSS WILD-TYPE                                        7
D44V8, multiclass
                                                                   clus
vv                                                                  2Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               0
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  2Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          148
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                69
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 53
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  27
  2Q LOSS WILD-TYPE   4 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   27
  2Q LOSS WILD-TYPE    4  362
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2                 4
  YES              27               362
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    22   3   2   0
  2Q LOSS WILD-TYPE 296  13  16  25
D44V10, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              22               296
  R1               3                13
  R2               2                16
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  2Q LOSS MUTATED      10                         1
  2Q LOSS WILD-TYPE    78                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           0    12
  2Q LOSS WILD-TYPE                                         1   231
D44V12, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                                  10                78
  BLACK OR AFRICAN AMERICAN                               1                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  12               231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    49  25
  3P LOSS WILD-TYPE 193  97
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               74               290 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               25                97 
$`3P LOSS MUTATED`
TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 
       10.13         7.00        31.20        35.24        15.42        28.01 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8483 
        0.69        18.71        17.49         0.69         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A452 
        0.72         9.21        20.22        15.68         0.62         0.66 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J8 
       22.26         0.92        12.89         0.72         0.53        13.51 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-A48A 
       20.42         1.15        13.64         0.07         0.13         0.13 
TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4455 
       20.02         7.99         8.05        54.08         4.01        12.03 
TCGA-CG-4466 TCGA-CG-5725 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-6521 TCGA-D7-6525 
       18.97        15.02         4.01        12.66        18.54         5.95 
TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-A6EX TCGA-EQ-5647 TCGA-EQ-8122 TCGA-FP-7829 
       17.19        15.22        11.31         0.62         7.79        19.53 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8245 TCGA-HU-8249 
        3.02        17.06         0.56         1.55        12.59        14.17 
TCGA-HU-A4GC TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-IN-7806 TCGA-IN-A6RO TCGA-IN-A6RP 
        3.25         6.25        17.69        21.21         1.41         6.44 
TCGA-IN-A6RS TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7C1 TCGA-RD-A8N6 
        6.87         5.56        28.90         4.31        16.67         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8PJ TCGA-VQ-A8PY TCGA-VQ-A91X TCGA-VQ-A925 
        5.79        13.25         2.70        14.33         8.58         4.54 
TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       29.98         0.79 

$`3P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        13.12        13.68        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       21.11        30.90        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       23.93         0.69         0.16        18.54        12.43         0.95 
TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       12.76         0.82         1.32        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.72         0.26        12.95        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        3.72         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU 
        0.59        10.68        12.56         1.15         3.02        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
       13.51         0.79        14.17        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        0.46        20.65        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 
       13.15        13.18         0.30         0.07         0.07         0.07 
TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 
        0.07         0.10         0.10         0.10         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
       15.95         1.02        14.01        29.98        47.05        19.07 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
       21.99         9.01         7.07        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
      105.07        12.03        28.96        79.07        65.10        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.36        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.84        18.61        17.85         4.14        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19         0.23         6.97        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 
       11.24        11.44         9.76         2.96        15.65         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13        16.24         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         8.12         0.39        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
       13.58         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
       10.19         0.26         2.10        12.95        19.36        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-8462 
        9.67         8.88         8.81        27.42         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR 
        3.39        18.38         5.36         5.19        13.08         6.74 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56         1.81         2.53        60.56         3.72        19.73 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       11.05         8.61         4.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44        35.61        16.87 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        37.74         5.46        13.02        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       19.30        23.57        64.57        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
        8.68        49.25        20.81         1.71         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
       44.25         8.61        55.43         6.58         5.72        40.08 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       21.11         4.21 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            54.08            122.30 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            8.760            11.885 
[1] "0.1 - 54.1 (8.8)"   "0.1 - 122.3 (11.9)"
[1] "hr=" "1.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         0        3        8        5         7        10
  3P LOSS WILD-TYPE       2       10       31       26        29        39
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           0         18         11          6        7
  3P LOSS WILD-TYPE         3         59         44         31       30
D45V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                10
  STAGE IB                 8                31
  STAGE II                 5                26
  STAGE IIA                7                29
  STAGE IIB               10                39
  STAGE III                0                 3
  STAGE IIIA              18                59
  STAGE IIIB              11                44
  STAGE IIIC               6                31
  STAGE IV                 7                30
[1] 11  2
[1] TRUE
[1] "dimension of 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     4  16  34  21
  3P LOSS WILD-TYPE  17  71 139  83
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               4                17
  T2              16                71
  T3              34               139
  T4              21                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P LOSS MUTATED    21  19  25  10
  3P LOSS WILD-TYPE 101  88  50  69
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              21               101
  N1              19                88
  N2              25                50
  N3              10                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  3P LOSS MUTATED    64   6   6
  3P LOSS WILD-TYPE 289  18  12
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              64               289
  M1               6                18
  MX               6                12
[1] 3 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    29  47
  3P LOSS WILD-TYPE 122 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     29   47
  3P LOSS WILD-TYPE  122  197
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              29               122
  MALE                47               197
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3P LOSS MUTATED                                       8
  3P LOSS WILD-TYPE                                    57
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                       31
  3P LOSS WILD-TYPE                                                    126
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                                  19
  3P LOSS WILD-TYPE                                                                50
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  3P LOSS MUTATED                                                 12
  3P LOSS WILD-TYPE                                               52
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3P LOSS MUTATED                                                          4
  3P LOSS WILD-TYPE                                                       17
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  3P LOSS MUTATED                                                           1
  3P LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3P LOSS MUTATED                                          1
  3P LOSS WILD-TYPE                                        8
D45V8, multiclass
                                                                   clus
vv                                                                  3P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  3P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  75
  3P LOSS WILD-TYPE   5 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   75
  3P LOSS WILD-TYPE    5  314
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                1                 5
  YES              75               314
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    65   2   5   1
  3P LOSS WILD-TYPE 253  14  13  24
D45V10, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              65               253
  R1               2                14
  R2               5                13
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED      16                         0
  3P LOSS WILD-TYPE    72                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           0    48
  3P LOSS WILD-TYPE                                         1   195
D45V12, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                                  16                72
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  48               195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    29  13
  3Q LOSS WILD-TYPE 213 109
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               42               322 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13               109 
$`3Q LOSS MUTATED`
TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7959 TCGA-BR-8077 
       10.13        35.24        15.42        28.01        18.71         0.69 
TCGA-BR-8289 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8687 TCGA-BR-A452 
        0.26         5.39         9.21        20.22         0.62         0.66 
TCGA-BR-A4CQ TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QI 
       22.26        12.89         0.72        13.51         1.15        13.64 
TCGA-CD-A48A TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4466 TCGA-CG-5725 TCGA-D7-5578 
        0.13        54.08         4.01        18.97        15.02        12.66 
TCGA-D7-6526 TCGA-D7-A6EX TCGA-EQ-5647 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A4BF 
       17.19        11.31         0.62        19.53        17.06         1.55 
TCGA-HU-8249 TCGA-HU-A4GU TCGA-IN-7806 TCGA-IN-A6RO TCGA-IN-A6RS TCGA-KB-A6F5 
       14.17         6.25        21.21         1.41         6.87         5.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-VQ-A8DV TCGA-VQ-A8PY TCGA-VQ-A91X TCGA-VQ-AA6B 
       28.90         4.31        13.25        14.33         8.58        29.98 

$`3Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.12        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
        9.21        24.76        23.93         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.95         0.69        12.76        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        1.32        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       14.79         0.69         0.26        15.85         3.72         0.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         0.59 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS 
       15.68        10.68        12.56         1.15         3.02         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.41        13.51         0.79        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL 
        0.66        19.36         0.46        20.65        20.42        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.07         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         6.35         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.10         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 
       15.95         1.02         7.99         8.05        14.01        29.98 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 
       47.05        19.07        12.03        21.99         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.36        11.93        19.13        20.55        18.84        18.54 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       18.61        17.85         5.95         4.14        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19         0.23         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.24        11.44         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 
        4.34         7.40         7.13         7.79        16.24         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27         8.12         0.39         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A8CX 
       22.29        59.54         5.03        13.58         0.56         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       12.30         9.67         8.88         8.81        27.42         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38         5.36         5.19        13.08 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 
        6.44         6.74         5.56         1.81         2.53        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        3.72        19.73        11.05         8.61         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       57.44         8.94        35.61        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       37.74         5.46        13.02        31.10        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       23.77         7.73        19.07        33.63        46.26        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       19.30        23.57        64.57        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
        8.68        49.25        20.81         1.71         7.36         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
       44.25         8.61        55.43         4.54         6.58         5.72 
TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08        21.11         4.21         0.79 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.13              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            54.08            122.30 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           12.775            11.555 
[1] "0.1 - 54.1 (12.8)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1"  
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         0        3        3        1         5         7
  3Q LOSS WILD-TYPE       2       10       36       30        31        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           0         11          6          3        4
  3Q LOSS WILD-TYPE         3         66         49         34       33
D46V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                10
  STAGE IB                 3                36
  STAGE II                 1                30
  STAGE IIA                5                31
  STAGE IIB                7                42
  STAGE III                0                 3
  STAGE IIIA              11                66
  STAGE IIIB               6                49
  STAGE IIIC               3                34
  STAGE IV                 4                33
[1] 11  2
[1] TRUE
[1] "dimension of 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     3   3  24  13
  3Q LOSS WILD-TYPE  18  84 149  91
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               3                18
  T2               3                84
  T3              24               149
  T4              13                91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q LOSS MUTATED    13  11  13   6
  3Q LOSS WILD-TYPE 109  96  62  73
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              13               109
  N1              11                96
  N2              13                62
  N3               6                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  3Q LOSS MUTATED    40   3   1
  3Q LOSS WILD-TYPE 313  21  17
D46V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0              40               313
  M1               3                21
  MX               1                17
[1] 3 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    17  27
  3Q LOSS WILD-TYPE 134 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     17   27
  3Q LOSS WILD-TYPE  134  217
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              17               134
  MALE                27               217
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  3Q LOSS MUTATED                                       2
  3Q LOSS WILD-TYPE                                    63
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                       22
  3Q LOSS WILD-TYPE                                                    135
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                                  11
  3Q LOSS WILD-TYPE                                                                58
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  3Q LOSS MUTATED                                                  6
  3Q LOSS WILD-TYPE                                               58
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  3Q LOSS MUTATED                                                          2
  3Q LOSS WILD-TYPE                                                       19
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  3Q LOSS MUTATED                                                           0
  3Q LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  3Q LOSS MUTATED                                          1
  3Q LOSS WILD-TYPE                                        8
D46V8, multiclass
                                                                   clus
vv                                                                  3Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              11
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  3Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                58
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  44
  3Q LOSS WILD-TYPE   6 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   44
  3Q LOSS WILD-TYPE    6  345
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                0                 6
  YES              44               345
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    38   2   2   1
  3Q LOSS WILD-TYPE 280  14  16  24
D46V10, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              38               280
  R1               2                14
  R2               2                16
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED       8                         0
  3Q LOSS WILD-TYPE    80                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           0    31
  3Q LOSS WILD-TYPE                                         1   212
D46V12, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                                   8                80
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  31               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"

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    88  46
  4P LOSS WILD-TYPE 154  76
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              134               230 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               46                76 
$`4P LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7197 
        6.61         9.57        10.13         0.62        31.20         9.21 
TCGA-BR-7704 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       35.24         0.69        18.54         0.69        18.71        17.49 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.69         0.49         0.26        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 
        7.40        19.50        22.19         2.96        14.04        14.79 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 
        3.72         5.39         9.21        20.22         0.49        11.54 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        0.59        10.68         0.66        22.26         0.92         0.72 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4QI TCGA-CD-5799 TCGA-CD-5802 
        0.66        13.51        20.65        13.64         3.25         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.07         0.07         0.07         0.10         0.13         0.13 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 
        0.13         0.13         0.13         0.13         0.10        20.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 
        7.99         8.05        54.08         4.01        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5725 TCGA-CG-5727 
       12.03        18.97         7.07        30.97        15.02        79.07 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 
       19.13        20.55        17.19         4.14        15.22        11.31 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 
       19.50         0.23        16.44        11.31         7.40         0.62 
TCGA-EQ-8122 TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF TCGA-FP-A8CX 
        7.79         8.12         3.02        17.06         1.55         0.23 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       26.47         1.51         5.92        12.59        14.17        12.10 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       22.75        25.81         8.98         6.25         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-8663 
       12.95        17.69         9.67        27.42        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A6F5 
        5.36         1.41         6.44         6.74         2.53         5.56 
TCGA-KB-A6F7 TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
       60.56         4.31        11.05        16.67        37.91       115.69 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        35.61         5.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PZ 
       31.10        21.73         7.73        46.26         2.70        59.18 
TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       28.70         8.58         9.73        44.25         8.61         4.54 
TCGA-VQ-AA6B TCGA-VQ-AA6J 
       29.98        21.11 

$`4P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         6.61        34.68        15.95        13.12 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.68         7.00        39.12         0.82        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         8.98        21.11        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       32.94        12.82        24.76        23.93        15.42        28.01 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 
        0.16        12.43         0.95        12.76         0.82         1.32 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8360 
       12.26        20.55         0.72         0.26        12.95         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
        0.36         0.26         0.95        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 
        0.36        19.17         0.69         0.26        15.85         0.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
        7.53        15.81        16.44        15.68         0.62        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        1.15         3.02        13.41        13.51        12.89         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
       14.17         0.53        12.82        19.36         0.46        20.42 
TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
        1.15        11.57         5.13         2.83        13.15        13.18 
TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        0.10         6.35         0.07         0.10         0.10         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 
       27.02        15.95         1.02        14.01        29.98        21.99 
TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        9.01        12.00        22.98         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        11.93        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
        5.95        15.98        12.79        10.55        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       16.80        17.19         6.97        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B 
       11.44         9.76         2.96        15.65         4.34         7.13 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 
       16.24         6.58        14.47        72.23        21.27         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       19.53        22.29        59.54         5.03        13.58         0.56 
TCGA-HF-A5NB TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       18.08        14.27        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GH 
        5.59        12.30        11.84        24.20         3.25        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 
       21.37        29.98         0.10         6.51        10.19        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI 
       12.30         8.88         8.81        21.21         3.45        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A93H 
        5.19        13.08         6.87         5.56         1.81        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        3.72        19.73         8.61         4.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT 
      116.38        71.38        57.44        16.87         0.92        37.74 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PK 
       22.36        23.77        19.07        33.63        16.31        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
        1.87         9.27        23.41        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       64.57        14.33        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
        1.71         7.36        55.43         6.58         5.72        40.08 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.07              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           115.69            122.30 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            9.095            12.345 
[1] "0.1 - 115.7 (9.1)"  "0.1 - 122.3 (12.3)"
[1] "hr=" "1.1"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         0        2       12       16        18        14
  4P LOSS WILD-TYPE       2       11       27       15        18        35
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           0         33         20         16       11
  4P LOSS WILD-TYPE         3         44         35         21       26
D47V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                11
  STAGE IB                12                27
  STAGE II                16                15
  STAGE IIA               18                18
  STAGE IIB               14                35
  STAGE III                0                 3
  STAGE IIIA              33                44
  STAGE IIIB              20                35
  STAGE IIIC              16                21
  STAGE IV                11                26
[1] 11  2
[1] TRUE
[1] "dimension of 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    5 28 76 35
  4P LOSS WILD-TYPE 16 59 97 69
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               5                16
  T2              28                59
  T3              76                97
  T4              35                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4P LOSS MUTATED   42 39 34 28
  4P LOSS WILD-TYPE 80 68 41 51
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              42                80
  N1              39                68
  N2              34                41
  N3              28                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  4P LOSS MUTATED   133   6   8
  4P LOSS WILD-TYPE 220  18  10
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0             133               220
  M1               6                18
  MX               8                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    55  92
  4P LOSS WILD-TYPE  96 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     55   92
  4P LOSS WILD-TYPE   96  152
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              55                96
  MALE                92               152
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  4P LOSS MUTATED                                      20
  4P LOSS WILD-TYPE                                    45
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                       55
  4P LOSS WILD-TYPE                                                    102
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                                  29
  4P LOSS WILD-TYPE                                                                40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  4P LOSS MUTATED                                                 27
  4P LOSS WILD-TYPE                                               37
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  4P LOSS MUTATED                                                          8
  4P LOSS WILD-TYPE                                                       13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  4P LOSS MUTATED                                                           2
  4P LOSS WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  4P LOSS MUTATED                                          6
  4P LOSS WILD-TYPE                                        3
D47V8, multiclass
                                                                   clus
vv                                                                  4P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         55
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              29
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               27
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        6
                                                                   clus
vv                                                                  4P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          102
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                40
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 37
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          3
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     3 144
  4P LOSS WILD-TYPE   3 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3  144
  4P LOSS WILD-TYPE    3  245
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                3                 3
  YES             144               245
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED   117   6   6   8
  4P LOSS WILD-TYPE 201  10  12  17
D47V10, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0             117               201
  R1               6                10
  R2               6                12
  RX               8                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"
D47V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED      37                         2
  4P LOSS WILD-TYPE    51                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           0    87
  4P LOSS WILD-TYPE                                         1   156
D47V12, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                                  37                51
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  87               156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    88  46
  4Q LOSS WILD-TYPE 154  76
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              134               230 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               46                76 
$`4Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 
        6.61        10.13         7.00         0.62        31.20        35.24 
TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        0.69        18.54         0.69        18.71        17.49         0.82 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
        0.69         0.49         0.26        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8373 
        7.40        19.50        22.19         2.96        14.04        14.79 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8677 TCGA-BR-8678 
        3.72         5.39         9.21        20.22         0.49        11.54 
TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        0.59        10.68         0.66        22.26         0.92         0.72 
TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
        0.66        13.51        20.65         1.15        13.64         3.25 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8532 
        0.30         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         0.13         0.13         0.13         0.13         0.13 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
        0.10        20.02         7.99         8.05        54.08         4.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5725 
       47.05        19.07        12.03        18.97        30.97        15.02 
TCGA-CG-5727 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 
       79.07         4.01        55.04        19.13        20.55        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-8575 
        4.14        15.22        15.98        11.31        19.50         0.23 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-A72C 
       16.44        11.31         7.40         0.62         7.79         8.12 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8243 
        3.02        17.06         1.55         0.23         1.51         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY 
       12.59        12.10        22.75         8.98         6.25         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8462 
        2.10        12.95        17.69         9.67        27.42        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT 
        3.39         5.36         1.41         6.44         6.74         5.56 
TCGA-IP-7968 TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 
        2.53         4.31        11.05        16.67        37.91       115.69 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94        35.61         5.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PZ 
       31.10        21.73         7.73        46.26         2.70        59.18 
TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       28.70         8.58         9.73        44.25         8.61         4.54 
TCGA-VQ-AA6B TCGA-VQ-AA6J 
       29.98        21.11 

$`4Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 
       13.12        13.68        39.12         0.82        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         8.98        21.11        30.90 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       32.94        12.82         9.21        24.76        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-8060 
       28.01         0.16        12.43         0.95        12.76         1.32 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8360 
       12.26        20.55         0.72         0.26        12.95         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
        0.36         0.26         0.95        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8484 
        0.36        19.17         0.69         0.26        15.85         0.72 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
        7.53        15.81        16.44        15.68         0.62        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        1.15         3.02        13.41        13.51        12.89         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
       14.17         0.53        12.82        19.36         0.46        20.42 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8524 
       11.57         5.13         2.83        13.15        13.18         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.13         0.16         0.10         0.10         6.35 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.07         0.10         0.10         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 
        1.02        14.01        29.98        21.99         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5728 
        6.02         0.99       105.07        12.03        28.96        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 
       21.07         7.99        12.36        12.66        11.93        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6817 TCGA-D7-6818 
       18.54        18.61        17.85         5.95        12.79        10.55 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 
       12.33        24.72        16.80        17.19         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.24        11.44         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        4.34         7.13        16.24         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         0.39        19.53        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 
       13.58         0.56        18.08        26.47        14.27        14.17 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-HU-A4H5 
       29.98         0.10         6.51        10.19        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-A6RI TCGA-IN-A6RL 
        8.88         8.81        21.21         3.45        18.38         5.19 
TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
       13.08         6.87         1.81         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 
        3.72        19.73         8.61         4.67       122.30        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT 
      116.38        71.38        57.44        16.87         0.92        37.74 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PK 
       22.36        23.77        19.07        33.63        16.31        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
        1.87         9.27        23.41        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       64.57        14.33        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
        1.71         7.36        55.43         6.58         5.72        40.08 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.07              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           115.69            122.30 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            8.350            12.495 
[1] "0.1 - 115.7 (8.3)"  "0.1 - 122.3 (12.5)"
[1] "hr=" "1.2"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         0        2       10       15        16        16
  4Q LOSS WILD-TYPE       2       11       29       16        20        33
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           1         32         21         16       12
  4Q LOSS WILD-TYPE         2         45         34         21       25
D48V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                11
  STAGE IB                10                29
  STAGE II                15                16
  STAGE IIA               16                20
  STAGE IIB               16                33
  STAGE III                1                 2
  STAGE IIIA              32                45
  STAGE IIIB              21                34
  STAGE IIIC              16                21
  STAGE IV                12                25
[1] 11  2
[1] TRUE
[1] "dimension of 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     4  30  71  37
  4Q LOSS WILD-TYPE  17  57 102  67
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               4                17
  T2              30                57
  T3              71               102
  T4              37                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  4Q LOSS MUTATED   38 42 34 28
  4Q LOSS WILD-TYPE 84 65 41 51
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              38                84
  N1              42                65
  N2              34                41
  N3              28                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  4Q LOSS MUTATED   132   7   6
  4Q LOSS WILD-TYPE 221  17  12
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0             132               221
  M1               7                17
  MX               6                12
[1] 3 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    59  86
  4Q LOSS WILD-TYPE  92 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     59   86
  4Q LOSS WILD-TYPE   92  158
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              59                92
  MALE                86               158
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  4Q LOSS MUTATED                                      20
  4Q LOSS WILD-TYPE                                    45
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                       54
  4Q LOSS WILD-TYPE                                                    103
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                                  30
  4Q LOSS WILD-TYPE                                                                39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  4Q LOSS MUTATED                                                 26
  4Q LOSS WILD-TYPE                                               38
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  4Q LOSS MUTATED                                                          8
  4Q LOSS WILD-TYPE                                                       13
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  4Q LOSS MUTATED                                                           2
  4Q LOSS WILD-TYPE                                                         6
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  4Q LOSS MUTATED                                          5
  4Q LOSS WILD-TYPE                                        4
D48V8, multiclass
                                                                   clus
vv                                                                  4Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         54
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              30
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               26
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        5
                                                                   clus
vv                                                                  4Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          103
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                39
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 38
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     3 142
  4Q LOSS WILD-TYPE   3 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3  142
  4Q LOSS WILD-TYPE    3  247
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                3                 3
  YES             142               247
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED   117   5   7   6
  4Q LOSS WILD-TYPE 201  11  11  19
D48V10, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             117               201
  R1               5                11
  R2               7                11
  RX               6                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"
D48V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED      36                         2
  4Q LOSS WILD-TYPE    52                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           0    87
  4Q LOSS WILD-TYPE                                         1   156
D48V12, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                                  36                52
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  87               156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    27  21
  5P LOSS WILD-TYPE 215 101
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               48               316 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               21               101 
$`5P LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8295 
        6.61         7.00         0.62        12.76        18.71         1.55 
TCGA-BR-8369 TCGA-BR-8483 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ 
       14.04         5.39         0.59        10.68         0.66        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-8535 TCGA-CD-A4MH 
        0.92         0.72        13.64        13.15         0.13         0.10 
TCGA-CG-4440 TCGA-CG-4449 TCGA-D7-6520 TCGA-D7-6815 TCGA-F1-6875 TCGA-FP-8631 
        4.01        19.07        18.84        15.98        72.23         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8610 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
        1.55         5.92         0.76        11.77         8.98         6.25 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RP 
       17.69         9.67        21.21        18.81         5.19         6.44 
TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A8MW TCGA-SW-A7EB TCGA-VQ-A8DZ 
       60.56        28.90         4.31        37.91         5.79        13.02 
TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-ZQ-A9CR 
        7.73         2.70         1.71         9.73         8.61         0.79 

$`5P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.12        10.13        13.68        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-8058 TCGA-BR-8059 
       18.54        12.43         0.95         0.69        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 
        1.32         0.69        12.26         0.49        20.55         0.72 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
        0.26        12.95         0.26        16.31         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        13.74         4.31         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       14.79         0.69         0.26        15.85         3.72         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 
       16.44        15.68         0.62        12.56         1.15         3.02 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.82         0.66        19.36        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
       20.42         1.15        11.57         5.13         2.83         3.25 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.13         0.07         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
       14.01        29.98        47.05        12.03        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       18.97         7.07        12.00        22.98        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
       12.03        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       55.04        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        20.55        18.54        18.61        17.85         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19         4.14        15.22        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
        6.97        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76         2.96        15.65         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.13         0.62         7.79        16.24         6.58        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27         8.12         0.39        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
       26.47         1.51        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       12.10        10.62        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       19.36        12.30         8.88         8.81        27.42         3.45 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR 
        3.39        18.38         5.36        13.08         1.41         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UG 
        6.87         5.56         1.81         2.53         5.56         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
       19.73        11.05         8.61         4.67        16.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV 
       35.61        16.87         0.92        37.74         5.46        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       31.10        21.73        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W 
       28.70        11.70         8.68        49.25        20.81         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
        8.58        44.25        55.43         4.54         6.58         5.72 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
       40.08        29.98        21.11         4.21 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.10              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            72.23            122.30 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            7.365            12.030 
[1] "0.1 - 72.2 (7.4)"   "0.1 - 122.3 (12.0)"
[1] "hr=" "1.6"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         0        3        1        2         5         9
  5P LOSS WILD-TYPE       2       10       38       29        31        40
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           0         14          5          5        4
  5P LOSS WILD-TYPE         3         63         50         32       33
D49V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                10
  STAGE IB                 1                38
  STAGE II                 2                29
  STAGE IIA                5                31
  STAGE IIB                9                40
  STAGE III                0                 3
  STAGE IIIA              14                63
  STAGE IIIB               5                50
  STAGE IIIC               5                32
  STAGE IV                 4                33
[1] 11  2
[1] TRUE
[1] "dimension of 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     4   8  21  15
  5P LOSS WILD-TYPE  17  79 152  89
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               4                17
  T2               8                79
  T3              21               152
  T4              15                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P LOSS MUTATED    11  18  11   9
  5P LOSS WILD-TYPE 111  89  64  70
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              11               111
  N1              18                89
  N2              11                64
  N3               9                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  5P LOSS MUTATED    45   3   2
  5P LOSS WILD-TYPE 308  21  16
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0              45               308
  M1               3                21
  MX               2                16
[1] 3 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    17  33
  5P LOSS WILD-TYPE 134 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     17   33
  5P LOSS WILD-TYPE  134  211
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              17               134
  MALE                33               211
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5P LOSS MUTATED                                       3
  5P LOSS WILD-TYPE                                    62
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                       20
  5P LOSS WILD-TYPE                                                    137
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                                   7
  5P LOSS WILD-TYPE                                                                62
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  5P LOSS MUTATED                                                 14
  5P LOSS WILD-TYPE                                               50
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5P LOSS MUTATED                                                          3
  5P LOSS WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  5P LOSS MUTATED                                                           1
  5P LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5P LOSS MUTATED                                          2
  5P LOSS WILD-TYPE                                        7
D49V8, multiclass
                                                                   clus
vv                                                                  5P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  5P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0  50
  5P LOSS WILD-TYPE   6 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0   50
  5P LOSS WILD-TYPE    6  339
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                0                 6
  YES              50               339
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    41   1   4   3
  5P LOSS WILD-TYPE 277  15  14  22
D49V10, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              41               277
  R1               1                15
  R2               4                14
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5P LOSS MUTATED      15                         2
  5P LOSS WILD-TYPE    73                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           0    28
  5P LOSS WILD-TYPE                                         1   215
D49V12, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                                  15                73
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  28               215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    54  33
  5Q LOSS WILD-TYPE 188  89
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               87               277 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33                89 
$`5Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7716 
        6.61         7.00         0.62         9.21        35.24        28.01 
TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 
        0.95        12.76        18.71        12.95         0.26         1.55 
TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8687 
       14.04        14.79         5.39        11.54         0.59         0.62 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4QI 
       10.68         0.66        22.26         0.92         0.72        13.64 
TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8533 
       13.15        13.18         0.07         0.07         0.10         0.13 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4304 TCGA-CG-4440 
        0.13         0.13         0.13         0.10        27.02         4.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-5718 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6527 
       47.05        19.07         1.02        11.93        18.84         4.14 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6822 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-F1-6875 
       15.98        12.79        12.33        11.31         2.96        72.23 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8610 TCGA-HU-A4GC 
        0.56         1.55         5.92        12.59         0.76         3.25 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H6 
       22.75        11.77         8.98         6.25        17.69         9.67 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-KB-A6F7 
       27.42        21.21        18.81         5.19         6.44        60.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU 
       28.90         4.31        37.91         8.94         5.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ 
       13.25        13.02        31.10         7.73        46.26         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       17.85        23.57         1.71         9.73        44.25         8.61 
TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-ZQ-A9CR 
        4.54        40.08         0.79 

$`5Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.12        10.13        13.68        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 
       15.42         0.69         0.16        18.54        12.43         0.69 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49         0.82         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 
       20.55         0.72         0.26        16.31         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
        0.95        13.74         4.31         3.32         0.36        19.17 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 TCGA-BR-8485 
        0.69         0.26        15.85         3.72         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8686 
        0.20         7.53         0.49        15.81        16.44        15.68 
TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56         1.15         3.02        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       13.51         0.46        20.65        20.42         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83         3.25         0.30         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 
        0.07         0.13         0.16         0.10         0.10         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        6.35         0.13         0.13         0.07         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
       20.02         3.02        15.95         1.02         7.99         8.05 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
       54.08        14.01        29.98        12.03        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 
       18.97         7.07        12.00        22.98        30.97         6.97 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
       15.02        28.96        79.07        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        19.13        20.55 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.54        18.61        17.85         5.95        17.19        15.22 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
        0.23         6.97        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76        15.65         4.34         7.40         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 
        0.62         7.79        16.24         6.58        14.47        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 
        8.12         0.39        19.53         3.02        22.29        17.06 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       59.54         5.03        13.58         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
        1.51        14.27        14.17        11.41        12.10        10.62 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GF 
       24.30         5.59        12.30        11.84        24.20        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
        2.10        12.95        19.36        12.30         8.88         8.81 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO 
        3.45         3.39        18.38         5.36        13.08         1.41 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
        6.74         6.87         5.56         1.81         2.53         5.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        3.72        19.73        11.05         8.61         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8P2 
       35.61        16.87         0.92        37.74        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO 
       23.77        19.07        33.63        16.31         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        19.30        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W 
       28.70        11.70         8.68        49.25        20.81         7.36 
TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        8.58        55.43         6.58         5.72        29.98        21.11 
TCGA-ZA-A8F6 
        4.21 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.07              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            72.23            122.30 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             9.21             12.03 
[1] "0.1 - 72.2 (9.2)"   "0.1 - 122.3 (12.0)"
[1] "hr=" "1.3"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         0        3        6        8         7        13
  5Q LOSS WILD-TYPE       2       10       33       23        29        36
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           0         30          8          8        5
  5Q LOSS WILD-TYPE         3         47         47         29       32
D50V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                10
  STAGE IB                 6                33
  STAGE II                 8                23
  STAGE IIA                7                29
  STAGE IIB               13                36
  STAGE III                0                 3
  STAGE IIIA              30                47
  STAGE IIIB               8                47
  STAGE IIIC               8                29
  STAGE IV                 5                32
[1] 11  2
[1] TRUE
[1] "dimension of 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     4  18  43  23
  5Q LOSS WILD-TYPE  17  69 130  81
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               4                17
  T2              18                69
  T3              43               130
  T4              23                81
[1] 4 2
[1] TRUE
[1] "dimension of 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   23 31 21 14
  5Q LOSS WILD-TYPE 99 76 54 65
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              23                99
  N1              31                76
  N2              21                54
  N3              14                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  5Q LOSS MUTATED    84   4   2
  5Q LOSS WILD-TYPE 269  20  16
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              84               269
  M1               4                20
  MX               2                16
[1] 3 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    33  57
  5Q LOSS WILD-TYPE 118 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     33   57
  5Q LOSS WILD-TYPE  118  187
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              33               118
  MALE                57               187
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  5Q LOSS MUTATED                                       6
  5Q LOSS WILD-TYPE                                    59
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                       33
  5Q LOSS WILD-TYPE                                                    124
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                                  16
  5Q LOSS WILD-TYPE                                                                53
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  5Q LOSS MUTATED                                                 24
  5Q LOSS WILD-TYPE                                               40
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  5Q LOSS MUTATED                                                          5
  5Q LOSS WILD-TYPE                                                       16
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  5Q LOSS MUTATED                                                           3
  5Q LOSS WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  5Q LOSS MUTATED                                          3
  5Q LOSS WILD-TYPE                                        6
D50V8, multiclass
                                                                   clus
vv                                                                  5Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         33
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        3
                                                                   clus
vv                                                                  5Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          124
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1  89
  5Q LOSS WILD-TYPE   5 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1   89
  5Q LOSS WILD-TYPE    5  300
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                1                 5
  YES              89               300
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    76   3   5   3
  5Q LOSS WILD-TYPE 242  13  13  22
D50V10, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              76               242
  R1               3                13
  R2               5                13
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED      27                         2
  5Q LOSS WILD-TYPE    61                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           0    53
  5Q LOSS WILD-TYPE                                         1   190
D50V12, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                                  27                61
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  53               190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    31  16
  6P LOSS WILD-TYPE 211 106
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               47               317 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               16               106 
$`6P LOSS MUTATED`
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-7716 TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 
        6.18        10.13        28.01        22.26         0.72        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A48A 
       20.65         1.15         0.16         0.10         0.13         0.13 
TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 
        1.02        12.03        15.02        12.66        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F2 
       18.54         5.95        15.98        11.24        11.31        15.65 
TCGA-F1-A72C TCGA-FP-8099 TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU 
        8.12        17.06        26.47        22.75        11.77         6.25 
TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU 
       12.95        27.42         5.19         6.44         5.56         1.81 
TCGA-MX-A663 TCGA-RD-A7C1 TCGA-RD-A8N5 TCGA-VQ-A8DU TCGA-VQ-A8PU TCGA-VQ-A8PY 
        4.31        16.67        57.44         5.46        23.57        14.33 
TCGA-VQ-A91Q TCGA-VQ-A922 TCGA-VQ-A925 TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       20.81         8.61         4.54         4.21         0.79 

$`6P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.12        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 
       24.76        35.24        23.93        15.42         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.54        12.43         0.95         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49         0.82         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         0.72         0.26        12.95         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        1.55         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
       14.04         3.32         0.36        19.17        14.79         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        0.59        15.68         0.62        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        0.66         3.02         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.07         0.10         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         9.01        18.97         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 
      105.07        28.96        79.07        65.10         4.01        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 
       21.07         7.99        12.36        11.93        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       17.85        17.19         4.14        15.22        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
        0.23         6.97        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY 
        5.92        15.16        13.78        14.76        13.71        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
        9.76         2.96         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.79        16.24         6.58        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        0.39        19.53         3.02        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 
       13.58         0.56         1.55         0.23        18.08         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       24.20         3.25        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 
        0.10         6.51        10.19         0.26         2.10        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
       17.69        12.30         9.67         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.41         6.74         6.87         2.53         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
       28.90         3.72        19.73        11.05         8.61         4.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ 
        7.73        19.07        33.63        46.26        16.31         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        59.18        28.70        11.70         8.68        49.25 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 
        1.71         7.36         8.58         9.73        44.25        55.43 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        6.58         5.72        40.08        29.98        21.11 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.10              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            57.44            122.30 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            11.31             11.70 
[1] "0.1 - 57.4 (11.3)"  "0.1 - 122.3 (11.7)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         0        1        6        2         4         7
  6P LOSS WILD-TYPE       2       12       33       29        32        42
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           0         15          5          3        4
  6P LOSS WILD-TYPE         3         62         50         34       33
D51V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                12
  STAGE IB                 6                33
  STAGE II                 2                29
  STAGE IIA                4                32
  STAGE IIB                7                42
  STAGE III                0                 3
  STAGE IIIA              15                62
  STAGE IIIB               5                50
  STAGE IIIC               3                34
  STAGE IV                 4                33
[1] 11  2
[1] TRUE
[1] "dimension of 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     2  14  25   8
  6P LOSS WILD-TYPE  19  73 148  96
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               2                19
  T2              14                73
  T3              25               148
  T4               8                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P LOSS MUTATED    15  13  12   7
  6P LOSS WILD-TYPE 107  94  63  72
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              15               107
  N1              13                94
  N2              12                63
  N3               7                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  6P LOSS MUTATED    42   2   5
  6P LOSS WILD-TYPE 311  22  13
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              42               311
  M1               2                22
  MX               5                13
[1] 3 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    16  33
  6P LOSS WILD-TYPE 135 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     16   33
  6P LOSS WILD-TYPE  135  211
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              16               135
  MALE                33               211
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6P LOSS MUTATED                                       7
  6P LOSS WILD-TYPE                                    58
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                       21
  6P LOSS WILD-TYPE                                                    136
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                                   3
  6P LOSS WILD-TYPE                                                                66
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  6P LOSS MUTATED                                                 16
  6P LOSS WILD-TYPE                                               48
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6P LOSS MUTATED                                                          1
  6P LOSS WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  6P LOSS MUTATED                                                           0
  6P LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6P LOSS MUTATED                                          1
  6P LOSS WILD-TYPE                                        8
D51V8, multiclass
                                                                   clus
vv                                                                  6P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  6P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          136
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 48
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0  49
  6P LOSS WILD-TYPE   6 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   49
  6P LOSS WILD-TYPE    6  340
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                0                 6
  YES              49               340
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    43   0   2   3
  6P LOSS WILD-TYPE 275  16  16  22
D51V10, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              43               275
  R1               0                16
  R2               2                16
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6P LOSS MUTATED      11                         0
  6P LOSS WILD-TYPE    77                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           0    33
  6P LOSS WILD-TYPE                                         1   210
D51V12, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  33               210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    38  19
  6Q LOSS WILD-TYPE 204 103
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               57               307 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19               103 
$`6Q LOSS MUTATED`
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-7716 TCGA-BR-7722 TCGA-BR-8080 
        6.18        10.13         0.62        28.01         0.16         0.49 
TCGA-BR-A4CQ TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5803 TCGA-CD-8530 
       22.26        13.51        20.65         1.15         0.07         0.16 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-A48A TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-5719 
        0.10         0.13         0.13        29.98        12.03         1.02 
TCGA-CG-5724 TCGA-CG-5725 TCGA-D7-5578 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 
       12.03        15.02        12.66        20.55        18.84        18.54 
TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-8570 TCGA-D7-8576 TCGA-D7-A6EV TCGA-D7-A6EX 
        5.95        15.98        24.72         6.97        11.24        11.31 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-A72C TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       15.65         7.40         8.12        17.06        13.58         0.56 
TCGA-HJ-7597 TCGA-HU-A4GD TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4HD TCGA-IN-A6RL 
       26.47        22.75         6.25        17.69        27.42         5.19 
TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-A7NU TCGA-MX-A663 TCGA-RD-A7C1 TCGA-RD-A8MV 
        6.44         5.56         1.81         4.31        16.67       122.30 
TCGA-RD-A8N5 TCGA-VQ-A8DU TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91Q TCGA-VQ-A922 
       57.44         5.46        23.57        14.33        20.81         8.61 
TCGA-VQ-A925 TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.54         4.21         0.79 

$`6Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 
       13.12        13.68         7.00        39.12         0.82        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7851 
       35.24        23.93        15.42         0.69        18.54        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        0.95         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        1.32         0.69        12.26        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       12.95         0.26        16.31         1.55         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 
        6.18        19.50         0.36         0.26        22.19         2.96 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        5.39         0.72         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 
       15.81         2.14        13.45         0.20         7.53         0.49 
TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
       11.54        15.81        16.44         0.59        15.68         0.62 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       10.68        12.56         1.15         0.66         3.02         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
       13.41        13.51        12.89         0.79         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE 
        0.53        12.82         0.66        19.36         0.46        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.13         0.10         0.13         0.10         6.35 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        7.99         8.05        54.08         4.01        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       19.07        21.99         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       22.98        30.97         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
        0.99       105.07        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6518 
       55.04        21.07         7.99        12.36        11.93        19.13 
TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 
       18.61        17.85        17.19         4.14        15.22        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        12.33        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
        0.23        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ 
       15.16        13.78        14.76        13.71        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        2.96         4.34         7.13         0.62         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        6.58        14.47        72.23        21.27         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX 
        3.02        22.29        59.54         5.03         1.55         0.23 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 
       18.08         1.51         5.92        14.27        12.59        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        11.84        24.20         3.25        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 
        0.26         2.10        12.95        19.36        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS 
       18.38         5.36        13.08         1.41         6.74         6.87 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        28.90         3.72        19.73 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         8.61         4.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
      116.38        71.38         8.94        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        37.74        13.25        13.02        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       16.31         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       15.65        19.30        64.57        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
        8.68        49.25         1.71         7.36         8.58         9.73 
TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B 
       44.25        55.43         6.58         5.72        40.08        29.98 
TCGA-VQ-AA6J 
       21.11 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           122.30            116.38 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            11.24             11.70 
[1] "0.1 - 122.3 (11.2)" "0.1 - 116.4 (11.7)"
[1] "hr=" "1"  
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         0        1        6        4         4        11
  6Q LOSS WILD-TYPE       2       12       33       27        32        38
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           0         17          7          5        4
  6Q LOSS WILD-TYPE         3         60         48         32       33
D52V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                12
  STAGE IB                 6                33
  STAGE II                 4                27
  STAGE IIA                4                32
  STAGE IIB               11                38
  STAGE III                0                 3
  STAGE IIIA              17                60
  STAGE IIIB               7                48
  STAGE IIIC               5                32
  STAGE IV                 4                33
[1] 11  2
[1] TRUE
[1] "dimension of 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     2  16  33  10
  6Q LOSS WILD-TYPE  19  71 140  94
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               2                19
  T2              16                71
  T3              33               140
  T4              10                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q LOSS MUTATED    17  17  16  10
  6Q LOSS WILD-TYPE 105  90  59  69
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              17               105
  N1              17                90
  N2              16                59
  N3              10                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  6Q LOSS MUTATED    53   2   7
  6Q LOSS WILD-TYPE 300  22  11
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              53               300
  M1               2                22
  MX               7                11
[1] 3 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    20  42
  6Q LOSS WILD-TYPE 131 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     20   42
  6Q LOSS WILD-TYPE  131  202
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              20               131
  MALE                42               202
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  6Q LOSS MUTATED                                       8
  6Q LOSS WILD-TYPE                                    57
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                       26
  6Q LOSS WILD-TYPE                                                    131
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                                   6
  6Q LOSS WILD-TYPE                                                                63
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  6Q LOSS MUTATED                                                 18
  6Q LOSS WILD-TYPE                                               46
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  6Q LOSS MUTATED                                                          3
  6Q LOSS WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  6Q LOSS MUTATED                                                           0
  6Q LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  6Q LOSS MUTATED                                          1
  6Q LOSS WILD-TYPE                                        8
D52V8, multiclass
                                                                   clus
vv                                                                  6Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           8
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               6
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  6Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            57
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                63
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 46
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0  62
  6Q LOSS WILD-TYPE   6 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   62
  6Q LOSS WILD-TYPE    6  327
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                0                 6
  YES              62               327
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    53   1   2   4
  6Q LOSS WILD-TYPE 265  15  16  21
D52V10, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              53               265
  R1               1                15
  R2               2                16
  RX               4                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"
D52V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  6Q LOSS MUTATED      11                         0
  6Q LOSS WILD-TYPE    77                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           0    43
  6Q LOSS WILD-TYPE                                         1   200
D52V12, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                                  11                77
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  43               200
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    12   5
  7P LOSS WILD-TYPE 230 117
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               17               347 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5               117 
$`7P LOSS MUTATED`
TCGA-BR-7723 TCGA-BR-8678 TCGA-CG-4438 TCGA-CG-4443 TCGA-D7-6820 TCGA-D7-8573 
       18.54        11.54        54.08        29.98        11.31        19.50 
TCGA-D7-A6EX TCGA-FP-8631 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-IN-A6RN TCGA-IN-A7NU 
       11.31         0.56        11.77         6.25        13.08         1.81 
TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8PJ 
       37.91        35.61         5.46        13.02         2.70 

$`7P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.25         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01         0.69         0.16        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         0.49        20.55         0.72         0.26        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.26        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       14.79         0.69         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.72         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        2.14        13.45         0.20         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU 
        1.15         0.66         3.02        22.26         0.92        13.41 
TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.51        12.89         0.79         0.72        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.82         0.66        19.36        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         6.35 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        0.13         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        1.02         7.99         8.05         4.01        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03        21.99         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85         5.95        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
        4.14        15.22        15.98        12.79        10.55        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        17.19         0.23         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       14.76        13.71        11.24        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       15.65         4.34         7.40         7.13         0.62         7.79 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
       16.24         6.58        14.47        72.23        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39        19.53         3.02        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         1.55         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        1.51         5.92        14.27        12.59        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         8.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        17.69        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        8.88         8.81        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP 
        3.39        18.38         5.36         5.19         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.74         6.87         5.56         2.53         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT 
       28.90         3.72        19.73         4.31        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        4.67        16.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL 
       71.38        57.44         8.94        16.87         5.79         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       37.74        13.25        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK 
        7.73        19.07        33.63        46.26        16.31        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
        1.87         9.27        23.41        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       49.25        20.81         1.71         7.36         8.58         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
       44.25         8.61        55.43         4.54         6.58         5.72 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08        29.98        21.11         4.21         0.79 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.56              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            54.08            122.30 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            11.77             11.57 
[1] "0.6 - 54.1 (11.8)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.3"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         0        2        1        1         1         2
  7P LOSS WILD-TYPE       2       11       38       30        35        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           0          4          2          2        3
  7P LOSS WILD-TYPE         3         73         53         35       34
D53V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                11
  STAGE IB                 1                38
  STAGE II                 1                30
  STAGE IIA                1                35
  STAGE IIB                2                47
  STAGE III                0                 3
  STAGE IIIA               4                73
  STAGE IIIB               2                53
  STAGE IIIC               2                35
  STAGE IV                 3                34
[1] 11  2
[1] TRUE
[1] "dimension of 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     3   3   9   3
  7P LOSS WILD-TYPE  18  84 164 101
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               3                18
  T2               3                84
  T3               9               164
  T4               3               101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P LOSS MUTATED     4   4   6   4
  7P LOSS WILD-TYPE 118 103  69  75
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               4               118
  N1               4               103
  N2               6                69
  N3               4                75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  7P LOSS MUTATED    15   2   1
  7P LOSS WILD-TYPE 338  22  17
D53V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0              15               338
  M1               2                22
  MX               1                17
[1] 3 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     4  14
  7P LOSS WILD-TYPE 147 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      4   14
  7P LOSS WILD-TYPE  147  230
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               4               147
  MALE                14               230
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7P LOSS MUTATED                                       2
  7P LOSS WILD-TYPE                                    63
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                        6
  7P LOSS WILD-TYPE                                                    151
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                                   4
  7P LOSS WILD-TYPE                                                                65
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  7P LOSS MUTATED                                                  5
  7P LOSS WILD-TYPE                                               59
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7P LOSS MUTATED                                                          0
  7P LOSS WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  7P LOSS MUTATED                                                           0
  7P LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7P LOSS MUTATED                                          1
  7P LOSS WILD-TYPE                                        8
D53V8, multiclass
                                                                   clus
vv                                                                  7P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          6
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  7P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          151
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  18
  7P LOSS WILD-TYPE   6 371
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   18
  7P LOSS WILD-TYPE    6  371
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                 6
  YES              18               371
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    15   0   2   1
  7P LOSS WILD-TYPE 303  16  16  24
D53V10, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              15               303
  R1               0                16
  R2               2                16
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED       3                         1
  7P LOSS WILD-TYPE    85                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           0    11
  7P LOSS WILD-TYPE                                         1   232
D53V12, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                                   3                85
  BLACK OR AFRICAN AMERICAN                               1                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  11               232
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    19   7
  7Q LOSS WILD-TYPE 223 115
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               26               338 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7               115 
$`7Q LOSS MUTATED`
TCGA-BR-7723 TCGA-BR-8369 TCGA-BR-8678 TCGA-BR-A4CS TCGA-CD-A48C TCGA-CG-4438 
       18.54        14.04        11.54         0.92         0.13        54.08 
TCGA-CG-4443 TCGA-D7-6820 TCGA-D7-8575 TCGA-D7-A6EX TCGA-FP-7829 TCGA-FP-8631 
       29.98        11.31         0.23        11.31        19.53         0.56 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI 
       22.75        11.77         6.25         9.67        27.42        18.38 
TCGA-IN-A6RN TCGA-IN-A7NU TCGA-KB-A93H TCGA-RD-A8MW TCGA-RD-A8N9 TCGA-VQ-A8DU 
       13.08         1.81        28.90        37.91        35.61         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8PJ 
       13.02         2.70 

$`7Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.25         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 
       12.82         9.21        24.76        35.24        23.93        15.42 
TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 
       28.01         0.69         0.16        12.43         0.95         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
       12.76        18.71        17.49         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         0.49        20.55         0.72         0.26        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.26        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
       13.74         4.31         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         0.20         7.53         0.49        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        0.59        15.68         0.62        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        0.66         3.02        22.26        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       13.64        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.18         0.30         0.07         0.07         0.07         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.10         0.13         0.16         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.13         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        20.02 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        47.05        19.07        12.03        21.99 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85         5.95        17.19         4.14        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       12.79        10.55        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       17.19         6.97        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76         2.96        15.65         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.13         0.62         7.79        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         8.12         0.39         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX 
       17.06        59.54         5.03        13.58         1.55         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.17        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20         3.25        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       21.37        29.98         8.98         0.10         6.51        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        17.69        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
        5.36         5.19         1.41         6.44         6.74         6.87 
TCGA-IN-A7NT TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56         2.53         5.56        60.56         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.31        11.05         8.61         4.67        16.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 
       40.64       115.69       116.38        71.38        57.44         8.94 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E2 
       16.87         5.79         0.92        37.74        13.25        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       28.70        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         8.58         9.73        44.25         8.61        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        4.54         6.58         5.72        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.13              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            54.08            122.30 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           12.395            11.505 
[1] "0.1 - 54.1 (12.4)"  "0.1 - 122.3 (11.5)"
[1] "hr=" "1.4"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         0        2        2        2         1         6
  7Q LOSS WILD-TYPE       2       11       37       29        35        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           0          7          3          3        3
  7Q LOSS WILD-TYPE         3         70         52         34       34
D54V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 2                11
  STAGE IB                 2                37
  STAGE II                 2                29
  STAGE IIA                1                35
  STAGE IIB                6                43
  STAGE III                0                 3
  STAGE IIIA               7                70
  STAGE IIIB               3                52
  STAGE IIIC               3                34
  STAGE IV                 3                34
[1] 11  2
[1] TRUE
[1] "dimension of 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     4   3  18   4
  7Q LOSS WILD-TYPE  17  84 155 100
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               4                17
  T2               3                84
  T3              18               155
  T4               4               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q LOSS MUTATED     6   8   9   6
  7Q LOSS WILD-TYPE 116  99  66  73
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               6               116
  N1               8                99
  N2               9                66
  N3               6                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  7Q LOSS MUTATED    26   2   1
  7Q LOSS WILD-TYPE 327  22  17
D54V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0              26               327
  M1               2                22
  MX               1                17
[1] 3 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     8  21
  7Q LOSS WILD-TYPE 143 223
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      8   21
  7Q LOSS WILD-TYPE  143  223
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               8               143
  MALE                21               223
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  7Q LOSS MUTATED                                       3
  7Q LOSS WILD-TYPE                                    62
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                       11
  7Q LOSS WILD-TYPE                                                    146
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                                   4
  7Q LOSS WILD-TYPE                                                                65
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  7Q LOSS MUTATED                                                  9
  7Q LOSS WILD-TYPE                                               55
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  7Q LOSS MUTATED                                                          1
  7Q LOSS WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  7Q LOSS MUTATED                                                           0
  7Q LOSS WILD-TYPE                                                         8
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  7Q LOSS MUTATED                                          1
  7Q LOSS WILD-TYPE                                        8
D54V8, multiclass
                                                                   clus
vv                                                                  7Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         11
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  7Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          146
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  29
  7Q LOSS WILD-TYPE   6 360
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   29
  7Q LOSS WILD-TYPE    6  360
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                 6
  YES              29               360
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    25   0   2   1
  7Q LOSS WILD-TYPE 293  16  16  24
D54V10, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              25               293
  R1               0                16
  R2               2                16
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED       9                         1
  7Q LOSS WILD-TYPE    79                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           0    16
  7Q LOSS WILD-TYPE                                         1   227
D54V12, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                                   9                79
  BLACK OR AFRICAN AMERICAN                               1                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  16               227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    40  29
  8P LOSS WILD-TYPE 202  93
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               69               295 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               29                93 
$`8P LOSS MUTATED`
TCGA-BR-4191 TCGA-BR-6456 TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-7716 TCGA-BR-7723 
       18.35        10.13        13.84         1.25        28.01        18.54 
TCGA-BR-7958 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8680 
       12.76         0.69        12.95         1.48         0.36        15.81 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44U TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J8 
        0.59         0.62         1.15        12.89         0.72        13.51 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-8526 TCGA-CD-8533 TCGA-CD-A48C TCGA-CD-A4MH 
        1.15        13.64         0.07         0.13         0.13         0.10 
TCGA-CG-4301 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4475 
        3.02         7.99        54.08         4.01        19.07        22.98 
TCGA-CG-5724 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 
       12.03         4.01        55.04        18.54         4.14        15.22 
TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-A4YU TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-6177 
       24.72         0.23        16.44        15.65         7.40         6.58 
TCGA-FP-8099 TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8610 TCGA-HU-A4GU TCGA-HU-A4HD 
       17.06         5.92        14.17         0.76         6.25        27.42 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 
        1.41         6.44         6.74         1.81         2.53         5.56 
TCGA-RD-A7BT TCGA-RD-A8MV TCGA-RD-A8MW TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
        8.61       122.30        37.91        31.10         7.73        46.26 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Z TCGA-VQ-A925 
       17.85         1.87        20.81         1.71        44.25         4.54 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
       40.08        29.98        21.11 

$`8P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.12        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       32.78        13.22        16.14         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       23.93        15.42         0.69         0.16        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8078 
        0.69        18.71        17.49         0.82         1.32        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
        0.49        20.55         0.72         0.26         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 
        1.55         7.40         6.18        19.50         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39         0.72         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T 
        0.49        11.54        16.44        15.68        10.68        12.56 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.65        20.42        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        3.25        13.15        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.10         6.35         0.13         0.13 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 
        0.13         0.07         0.10         0.10        20.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
       15.95         1.02         8.05        14.01        29.98        47.05 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        0.99       105.07        15.02        28.96        79.07        65.10 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       20.55        18.84        18.61        17.85         5.95        17.19 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        10.55        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19         6.97        21.14        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B 
       11.31        11.44         9.76         2.96         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62         7.79        16.24        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
        8.12         0.39        19.53         3.02        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
        5.03        13.58         0.56         1.55         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        14.27        12.59        11.41        12.10 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
       10.62        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
        3.25        22.75        25.81        11.77        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        8.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
       12.95        19.36        17.69        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
        8.81        21.21         3.45        18.81         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 
        5.36         5.19        13.08         6.87         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BW 
       28.90         3.72        19.73         4.31        11.05         4.67 
TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       16.67        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        13.25        13.02        21.73        22.36        23.77 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       19.07        33.63        16.31         2.70         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A91X 
       28.70        11.70         8.68        49.25         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-ZA-A8F6 
        9.73         8.61        55.43         6.58         5.72         4.21 
TCGA-ZQ-A9CR 
        0.79 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.07              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           122.30            116.38 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             8.61             11.70 
[1] "0.1 - 122.3 (8.6)"  "0.1 - 116.4 (11.7)"
[1] "hr=" "1.4"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         1        2        3        4         4         6
  8P LOSS WILD-TYPE       1       11       36       27        32        43
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           0         15         17          8       10
  8P LOSS WILD-TYPE         3         62         38         29       27
D55V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  1                 1
  STAGE IA                 2                11
  STAGE IB                 3                36
  STAGE II                 4                27
  STAGE IIA                4                32
  STAGE IIB                6                43
  STAGE III                0                 3
  STAGE IIIA              15                62
  STAGE IIIB              17                38
  STAGE IIIC               8                29
  STAGE IV                10                27
[1] 11  2
[1] TRUE
[1] "dimension of 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     4   9  41  17
  8P LOSS WILD-TYPE  17  78 132  87
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               4                17
  T2               9                78
  T3              41               132
  T4              17                87
[1] 4 2
[1] TRUE
[1] "dimension of 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    13  19  19  20
  8P LOSS WILD-TYPE 109  88  56  59
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              13               109
  N1              19                88
  N2              19                56
  N3              20                59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  8P LOSS MUTATED    64   5   3
  8P LOSS WILD-TYPE 289  19  15
D55V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              64               289
  M1               5                19
  MX               3                15
[1] 3 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    20  52
  8P LOSS WILD-TYPE 131 192
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     20   52
  8P LOSS WILD-TYPE  131  192
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              20               131
  MALE                52               192
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8P LOSS MUTATED                                       3
  8P LOSS WILD-TYPE                                    62
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                       29
  8P LOSS WILD-TYPE                                                    128
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                                  17
  8P LOSS WILD-TYPE                                                                52
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  8P LOSS MUTATED                                                 18
  8P LOSS WILD-TYPE                                               46
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8P LOSS MUTATED                                                          1
  8P LOSS WILD-TYPE                                                       20
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  8P LOSS MUTATED                                                           1
  8P LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8P LOSS MUTATED                                          2
  8P LOSS WILD-TYPE                                        7
D55V8, multiclass
                                                                   clus
vv                                                                  8P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         29
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        2
                                                                   clus
vv                                                                  8P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          128
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 46
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1  71
  8P LOSS WILD-TYPE   5 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   71
  8P LOSS WILD-TYPE    5  318
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                1                 5
  YES              71               318
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED    59   3   6   2
  8P LOSS WILD-TYPE 259  13  12  23
D55V10, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              59               259
  R1               3                13
  R2               6                12
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8P LOSS MUTATED      16                         2
  8P LOSS WILD-TYPE    72                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           1    41
  8P LOSS WILD-TYPE                                         0   202
D55V12, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                                  16                72
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  41               202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    14  11
  8Q LOSS WILD-TYPE 228 111
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               339 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               111 
$`8Q LOSS MUTATED`
TCGA-BR-4191 TCGA-BR-6705 TCGA-BR-8286 TCGA-BR-A4J8 TCGA-BR-A4QI TCGA-CD-A48C 
       18.35        13.84        12.95        13.51        13.64         0.13 
TCGA-CD-A4MH TCGA-CG-4440 TCGA-CG-4475 TCGA-CG-5724 TCGA-D7-6521 TCGA-D7-6527 
        0.10         4.01        22.98        12.03        18.54         4.14 
TCGA-D7-8570 TCGA-FP-8099 TCGA-HU-8249 TCGA-IN-A7NU TCGA-RD-A7BT TCGA-RD-A8MV 
       24.72        17.06        14.17         1.81         8.61       122.30 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PY TCGA-VQ-A91U TCGA-VQ-A925 TCGA-VQ-AA6B 
       17.85         1.87        14.33         1.71         4.54        29.98 
TCGA-VQ-AA6J 
       21.11 

$`8Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        0.62        32.78        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       18.71        17.49         0.82         1.32         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8291 
        0.49        20.55         0.72         0.26         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        1.55         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
       14.04         3.32         0.36        19.17        14.79         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 
        0.26        15.85         3.72         5.39         0.72         9.21 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        0.59        15.68         0.62        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       12.89         0.79         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.66        19.36         0.46        20.65        20.42         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.07         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 
       15.95         1.02         7.99         8.05        54.08        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
       29.98        47.05        19.07        12.03        21.99         9.01 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 
       18.97         7.07        12.00        30.97         6.97         1.02 
TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 
        1.02         0.99         6.02         0.99       105.07        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 
       18.84        18.61        17.85         5.95        17.19        15.22 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 
       15.98        12.79        10.55        11.31        12.33        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       19.50        17.19         0.23         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 
       13.71        11.24        11.31        11.44         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 
       15.65         4.34         7.40         7.13         0.62         7.79 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
       16.24         6.58        14.47        72.23        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        0.39        19.53         3.02        22.29        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         0.56         1.55         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        14.27        12.59        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       24.20         3.25        22.75        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX 
       29.98         8.98         0.10         6.51         6.25        10.19 
TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        0.26         2.10        12.95        19.36        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 
        9.67         8.88         8.81        27.42        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       18.81         3.39        18.38         5.36         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IP-7968 
        1.41         6.44         6.74         6.87         5.56         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        28.90         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         4.67        16.67        37.91        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        37.74         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       31.10        21.73        22.36        23.77         7.73        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP 
       33.63        46.26        16.31         2.70         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        19.30        23.57        64.57        59.18        28.70 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91X 
       11.70         8.68        49.25        20.81         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        9.73        44.25         8.61        55.43         6.58         5.72 
TCGA-VQ-AA68 TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       40.08         4.21         0.79 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.10              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           122.30            116.38 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            13.64             11.41 
[1] "0.1 - 122.3 (13.6)" "0.1 - 116.4 (11.4)"
[1] "hr=" "1.2"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         0        0        0        2         3         2
  8Q LOSS WILD-TYPE       2       13       39       29        33        47
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           0          5          7          1        4
  8Q LOSS WILD-TYPE         3         72         48         36       33
D56V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 0                13
  STAGE IB                 0                39
  STAGE II                 2                29
  STAGE IIA                3                33
  STAGE IIB                2                47
  STAGE III                0                 3
  STAGE IIIA               5                72
  STAGE IIIB               7                48
  STAGE IIIC               1                36
  STAGE IV                 4                33
[1] 11  2
[1] TRUE
[1] "dimension of 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     0   3  20   2
  8Q LOSS WILD-TYPE  21  84 153 102
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               0                21
  T2               3                84
  T3              20               153
  T4               2               102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q LOSS MUTATED     4   5   7   9
  8Q LOSS WILD-TYPE 118 102  68  70
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               4               118
  N1               5               102
  N2               7                68
  N3               9                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  8Q LOSS MUTATED    23   2   1
  8Q LOSS WILD-TYPE 330  22  17
D56V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0              23               330
  M1               2                22
  MX               1                17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     7  19
  8Q LOSS WILD-TYPE 144 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7   19
  8Q LOSS WILD-TYPE  144  225
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               7               144
  MALE                19               225
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  8Q LOSS MUTATED                                       2
  8Q LOSS WILD-TYPE                                    63
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                        9
  8Q LOSS WILD-TYPE                                                    148
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                                   7
  8Q LOSS WILD-TYPE                                                                62
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  8Q LOSS MUTATED                                                  5
  8Q LOSS WILD-TYPE                                               59
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  8Q LOSS MUTATED                                                          0
  8Q LOSS WILD-TYPE                                                       21
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  8Q LOSS MUTATED                                                           1
  8Q LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  8Q LOSS MUTATED                                          1
  8Q LOSS WILD-TYPE                                        8
D56V8, multiclass
                                                                   clus
vv                                                                  8Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          9
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               7
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  8Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          148
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                62
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 59
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  26
  8Q LOSS WILD-TYPE   6 363
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   26
  8Q LOSS WILD-TYPE    6  363
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 6
  YES              26               363
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    18   0   4   2
  8Q LOSS WILD-TYPE 300  16  14  23
D56V10, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              18               300
  R1               0                16
  R2               4                14
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  8Q LOSS MUTATED       4                         1
  8Q LOSS WILD-TYPE    84                         5
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           1    17
  8Q LOSS WILD-TYPE                                         0   226
D56V12, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                                   4                84
  BLACK OR AFRICAN AMERICAN                               1                 5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  17               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"

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    76  39
  9P LOSS WILD-TYPE 166  83
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              115               249 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               39                83 
$`9P LOSS MUTATED`
TCGA-BR-4191 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7704 
       18.35        13.68         7.00        31.20         9.21        35.24 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8077 
       28.01        18.54         0.95        17.49         1.32         0.69 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8483 
       12.95        16.31        22.19         2.96        14.04         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        0.72         9.21        20.22         0.59        15.68         0.62 
TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 TCGA-BR-A4J8 
        1.15        22.26         0.92         0.72         0.66        13.51 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5803 TCGA-CD-8524 
       20.65         1.15         3.25        13.15         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 
        0.07         0.07         0.07         0.10         0.13         6.35 
TCGA-CD-A48C TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 
        0.13         3.02        54.08         4.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5725 
       12.03        18.97        12.00         1.02         1.02        15.02 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
        4.01        55.04        12.66        11.93        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       18.54         5.95        17.19         4.14        15.98        12.79 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX 
        0.23         6.97        21.14        16.44        11.24        11.31 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 
        2.96         7.40         7.79        72.23         8.12        17.06 
TCGA-FP-8631 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GU 
        0.56         1.51         5.92        12.59        11.77         6.25 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
        9.67        27.42        21.21        18.81        18.38         5.36 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NT TCGA-KB-A93H TCGA-RD-A7BT TCGA-RD-A7BW 
        1.41         6.74         5.56        28.90         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E2 
       16.67        37.91         8.94         5.79        13.25        31.10 
TCGA-VQ-A8P5 TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PY 
        7.73         2.70        17.85         1.87        23.57        14.33 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-AA68 TCGA-VQ-AA6J 
       20.81         1.71         8.58         9.73        40.08        21.11 
TCGA-ZQ-A9CR 
        0.79 

$`9P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.12        10.13        39.12         0.82         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 
       30.90        32.94        12.82        24.76        23.93        15.42 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.69         0.16        12.43         0.69        12.76        18.71 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.82        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
        0.26         1.55         1.48         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
        0.36         0.26         0.95        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        3.72         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV 
       10.68        12.56         0.66         3.02        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 
       12.89         0.79        14.17         0.53        12.82        19.36 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42        13.64        11.57         5.13         2.83 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
       13.18         0.30         0.10         0.13         0.16         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
        0.13         0.10         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10         0.10        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4460 
        1.02         7.99         8.05        14.01        47.05        21.99 
TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5720 
        9.01         7.07        22.98        30.97         6.97         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6522 
       65.10        21.07         7.99        12.36        19.13        18.61 
TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       17.85        15.22        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       16.80        19.50        17.19        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ 
       15.16        13.78        14.76        13.71        11.44         9.76 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 
       15.65         4.34         7.13         0.62        16.24         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27         0.39        19.53         3.02        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB 
       59.54         5.03        13.58         1.55         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       26.47        14.27        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
        3.25        22.75        25.81        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        0.10         6.51        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 
       19.36        17.69        12.30         8.88         8.81         3.45 
TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NU 
        3.39         5.19        13.08         6.44         6.87         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        2.53         5.56        60.56         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
       11.05       122.30        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU 
       57.44        35.61        16.87         0.92        37.74         5.46 
TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       13.02        21.73        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       46.26        16.31         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       64.57        59.18        28.70        11.70         8.68        49.25 
TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        7.36        44.25         8.61        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 
        5.72        29.98         4.21 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            72.23            122.30 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             9.67             12.03 
[1] "0.1 - 72.2 (9.7)"   "0.1 - 122.3 (12.0)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         0        5       11       15        10        14
  9P LOSS WILD-TYPE       2        8       28       16        26        35
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           0         26         19          9       12
  9P LOSS WILD-TYPE         3         51         36         28       25
D57V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 5                 8
  STAGE IB                11                28
  STAGE II                15                16
  STAGE IIA               10                26
  STAGE IIB               14                35
  STAGE III                0                 3
  STAGE IIIA              26                51
  STAGE IIIB              19                36
  STAGE IIIC               9                28
  STAGE IV                12                25
[1] 11  2
[1] TRUE
[1] "dimension of 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     6  29  60  26
  9P LOSS WILD-TYPE  15  58 113  78
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               6                15
  T2              29                58
  T3              60               113
  T4              26                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  9P LOSS MUTATED   37 34 31 21
  9P LOSS WILD-TYPE 85 73 44 58
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              37                85
  N1              34                73
  N2              31                44
  N3              21                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  9P LOSS MUTATED   115   5   5
  9P LOSS WILD-TYPE 238  19  13
D57V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0             115               238
  M1               5                19
  MX               5                13
[1] 3 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    52  73
  9P LOSS WILD-TYPE  99 171
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     52   73
  9P LOSS WILD-TYPE   99  171
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              52                99
  MALE                73               171
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9P LOSS MUTATED                                      12
  9P LOSS WILD-TYPE                                    53
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                       49
  9P LOSS WILD-TYPE                                                    108
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                                  28
  9P LOSS WILD-TYPE                                                                41
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  9P LOSS MUTATED                                                 25
  9P LOSS WILD-TYPE                                               39
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9P LOSS MUTATED                                                          6
  9P LOSS WILD-TYPE                                                       15
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  9P LOSS MUTATED                                                           3
  9P LOSS WILD-TYPE                                                         5
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9P LOSS MUTATED                                          1
  9P LOSS WILD-TYPE                                        8
D57V8, multiclass
                                                                   clus
vv                                                                  9P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         49
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  9P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          108
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     3 122
  9P LOSS WILD-TYPE   3 267
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      3  122
  9P LOSS WILD-TYPE    3  267
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                3                 3
  YES             122               267
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED   106   3   6   5
  9P LOSS WILD-TYPE 212  13  12  20
D57V10, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             106               212
  R1               3                13
  R2               6                12
  RX               5                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"
D57V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9P LOSS MUTATED      27                         2
  9P LOSS WILD-TYPE    61                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           1    77
  9P LOSS WILD-TYPE                                         0   166
D57V12, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                                  27                61
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                  77               166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    52  26
  9Q LOSS WILD-TYPE 190  96
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               78               286 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               26                96 
$`9Q LOSS MUTATED`
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6803 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 
       13.68         7.00        31.20         9.21        28.01        18.54 
TCGA-BR-7901 TCGA-BR-8058 TCGA-BR-8060 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8364 
        0.95        17.49         1.32        12.95        16.31        22.19 
TCGA-BR-8365 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8686 TCGA-BR-A44U 
        2.96         5.39         0.72         9.21        15.68         1.15 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5803 
        0.92         0.72        13.51         1.15         3.25         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 
        0.07         0.07         0.07         0.10         0.13         6.35 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 
        0.13         0.10         3.02        54.08         4.01        29.98 
TCGA-CG-4455 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6527 
       12.03        20.55        18.84        18.54         5.95         4.14 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU 
       15.98        12.79         0.23         6.97        21.14        16.44 
TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-8099 
        2.96         7.40         7.79        72.23         8.12        17.06 
TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-8243 TCGA-HU-A4GH TCGA-HU-A4GU TCGA-HU-A4H0 
       13.58         0.56         5.92        11.77         6.25         2.10 
TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-KB-A93H TCGA-RD-A7C1 
       27.42        18.38         5.36         6.74        28.90        16.67 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8PJ 
       37.91         8.94         5.79        13.25        31.10         2.70 
TCGA-VQ-A8PK TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-AA68 TCGA-VQ-AA6J 
       17.85        20.81         1.71         9.73        40.08        21.11 

$`9Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       15.95        13.12        10.13        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7704 
       21.11        30.90        32.94        12.82        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 
       23.93        15.42         0.69         0.16        12.43         0.69 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       12.76        18.71         0.82         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
       20.55         0.72         0.26         0.26         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8366 
        7.40         6.18        19.50         0.36         0.26         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 
       14.79         0.69         0.26        15.85         3.72        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         0.59 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
        0.62        10.68        12.56         0.66         3.02        22.26 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
       12.82         0.66        19.36         0.46        20.65        20.42 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 
       13.64        11.57         5.13         2.83        13.15        13.18 
TCGA-CD-5802 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.30         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MG 
        0.13         0.10         0.13         0.13         0.13         0.07 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10         0.10        20.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 
        7.99         8.05        14.01        47.05        19.07        21.99 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6528 
       11.93        19.13        18.61        17.85        17.19        15.22 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       10.55        11.31        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       17.19        20.91        14.27         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 
       15.65         4.34         7.13         0.62        16.24         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       14.47        21.27         0.39        19.53         3.02        22.29 
TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       59.54         5.03         1.55         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 
        8.98         0.10         6.51        10.19         0.26        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        17.69        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RN 
       21.21         3.45        18.81         3.39         5.19        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        1.41         6.44         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS 
        5.56        60.56         3.72        19.73         4.31        11.05 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        8.61         4.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DT 
       71.38        57.44        35.61        16.87         0.92        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
        5.46        13.02        21.73        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO 
       19.07        33.63        46.26        16.31         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        19.30        23.57        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W 
       59.18        28.70        11.70         8.68        49.25         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        8.58        44.25         8.61        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        29.98         4.21         0.79 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            72.23            122.30 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            8.530            11.965 
[1] "0.1 - 72.2 (8.5)"   "0.1 - 122.3 (12.0)"
[1] "hr=" "1.1"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         0        3        8       11         8        11
  9Q LOSS WILD-TYPE       2       10       31       20        28        38
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           0         17         13          8        6
  9Q LOSS WILD-TYPE         3         60         42         29       31
D58V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 3                10
  STAGE IB                 8                31
  STAGE II                11                20
  STAGE IIA                8                28
  STAGE IIB               11                38
  STAGE III                0                 3
  STAGE IIIA              17                60
  STAGE IIIB              13                42
  STAGE IIIC               8                29
  STAGE IV                 6                31
[1] 11  2
[1] TRUE
[1] "dimension of 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     4  20  44  17
  9Q LOSS WILD-TYPE  17  67 129  87
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               4                17
  T2              20                67
  T3              44               129
  T4              17                87
[1] 4 2
[1] TRUE
[1] "dimension of 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   26 23 20 17
  9Q LOSS WILD-TYPE 96 84 55 62
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              26                96
  N1              23                84
  N2              20                55
  N3              17                62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  9Q LOSS MUTATED    80   3   5
  9Q LOSS WILD-TYPE 273  21  13
D58V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              80               273
  M1               3                21
  MX               5                13
[1] 3 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    31  57
  9Q LOSS WILD-TYPE 120 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     31   57
  9Q LOSS WILD-TYPE  120  187
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              31               120
  MALE                57               187
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  9Q LOSS MUTATED                                      11
  9Q LOSS WILD-TYPE                                    54
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                       38
  9Q LOSS WILD-TYPE                                                    119
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                                  17
  9Q LOSS WILD-TYPE                                                                52
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  9Q LOSS MUTATED                                                 17
  9Q LOSS WILD-TYPE                                               47
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  9Q LOSS MUTATED                                                          4
  9Q LOSS WILD-TYPE                                                       17
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  9Q LOSS MUTATED                                                           1
  9Q LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  9Q LOSS MUTATED                                          0
  9Q LOSS WILD-TYPE                                        9
D58V8, multiclass
                                                                   clus
vv                                                                  9Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                          11
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         38
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)              17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                               17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        0
                                                                   clus
vv                                                                  9Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            54
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     3  85
  9Q LOSS WILD-TYPE   3 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3   85
  9Q LOSS WILD-TYPE    3  304
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                3                 3
  YES              85               304
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    72   2   4   4
  9Q LOSS WILD-TYPE 246  14  14  21
D58V10, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              72               246
  R1               2                14
  R2               4                14
  RX               4                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"
D58V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  9Q LOSS MUTATED      22                         2
  9Q LOSS WILD-TYPE    66                         4
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           0    54
  9Q LOSS WILD-TYPE                                         1   189
D58V12, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                                  22                66
  BLACK OR AFRICAN AMERICAN                               2                 4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  54               189
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    28  21
  10P LOSS WILD-TYPE 214 101
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                49                315 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                21                101 
$`10P LOSS MUTATED`
TCGA-BR-4191 TCGA-BR-4267 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-7901 TCGA-BR-8060 
       18.35         6.18         7.00         0.82         0.95         1.32 
TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-A452 TCGA-BR-A4IY TCGA-CD-8525 
       16.31         2.96        20.22         0.66        12.89         0.07 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8533 TCGA-CG-4436 TCGA-CG-4455 TCGA-CG-4475 
        0.07         0.10         0.13         7.99        12.03        22.98 
TCGA-CG-5732 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 
       55.04        18.54         4.14        15.22        15.98        11.31 
TCGA-D7-8575 TCGA-D7-A6EV TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8631 TCGA-FP-A4BF 
        0.23        11.24         7.79        19.53         0.56         1.55 
TCGA-FP-A8CX TCGA-HU-8249 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RP 
        0.23        14.17        18.81        18.38         1.41         6.44 
TCGA-IN-A6RR TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DZ 
        6.74       115.69         8.94         5.79        37.74        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A928 TCGA-VQ-AA68 
       31.10        17.85        28.70        20.81         5.72        40.08 
TCGA-ZQ-A9CR 
        0.79 

$`10P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         9.57         6.61        34.68        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       10.13        13.68        39.12         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       23.93        15.42        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95         0.26         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.36         0.26        22.19         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        0.59        15.68         0.62        10.68        12.56         1.15 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        3.02        22.26         0.92        13.41        13.51         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8529 TCGA-CD-8530 
        0.30         0.07         0.07         0.07         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         6.35         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 
        8.05        54.08         4.01        14.01        29.98        47.05 
TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       19.07        21.99         9.01        18.97         7.07        12.00 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       11.93        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
        5.95        17.19        12.79        10.55        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       13.71        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 
        4.34         7.40         7.13         0.62        16.24         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27         8.12         0.39         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB 
       22.29        17.06        59.54         5.03        13.58        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 
       26.47         1.51         5.92        14.27        12.59        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       11.84        24.20         3.25        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 
       10.19         0.26         2.10        12.95        19.36        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       12.30         9.67         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RS 
        3.45         3.39         5.36         5.19        13.08         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        5.56         1.81         2.53         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       16.67       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
       57.44        35.61        16.87         0.92         5.46        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
       11.70         8.68        49.25         1.71         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        9.73        44.25         8.61        55.43         4.54         6.58 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
       29.98        21.11         4.21 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            115.69             122.30 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              8.94              11.77 
[1] "0.1 - 115.7 (8.9)"  "0.1 - 122.3 (11.8)"
[1] "hr=" "1.4"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         0        2        4        4         1        12
  10P LOSS WILD-TYPE       2       11       35       27        35        37
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           0         12          5          5        5
  10P LOSS WILD-TYPE         3         65         50         32       32
D59V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 11
  STAGE IB                  4                 35
  STAGE II                  4                 27
  STAGE IIA                 1                 35
  STAGE IIB                12                 37
  STAGE III                 0                  3
  STAGE IIIA               12                 65
  STAGE IIIB                5                 50
  STAGE IIIC                5                 32
  STAGE IV                  5                 32
[1] 11  2
[1] TRUE
[1] "dimension of 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     4  15  23   8
  10P LOSS WILD-TYPE  17  72 150  96
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                4                 17
  T2               15                 72
  T3               23                150
  T4                8                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P LOSS MUTATED    10  15  13  13
  10P LOSS WILD-TYPE 112  92  62  66
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               10                112
  N1               15                 92
  N2               13                 62
  N3               13                 66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  10P LOSS MUTATED    49   1   4
  10P LOSS WILD-TYPE 304  23  14
D59V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               49                304
  M1                1                 23
  MX                4                 14
[1] 3 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    18  36
  10P LOSS WILD-TYPE 133 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     18   36
  10P LOSS WILD-TYPE  133  208
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               18                133
  MALE                 36                208
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10P LOSS MUTATED                                       4
  10P LOSS WILD-TYPE                                    61
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                       20
  10P LOSS WILD-TYPE                                                    137
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                                   8
  10P LOSS WILD-TYPE                                                                61
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  10P LOSS MUTATED                                                 10
  10P LOSS WILD-TYPE                                               54
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10P LOSS MUTATED                                                          6
  10P LOSS WILD-TYPE                                                       15
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  10P LOSS MUTATED                                                           2
  10P LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10P LOSS MUTATED                                          3
  10P LOSS WILD-TYPE                                        6
D59V8, multiclass
                                                                   clus
vv                                                                  10P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          20
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  10P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           137
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  54
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  53
  10P LOSS WILD-TYPE   5 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   53
  10P LOSS WILD-TYPE    5  336
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 1                  5
  YES               53                336
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    44   3   1   5
  10P LOSS WILD-TYPE 274  13  17  20
D59V10, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               44                274
  R1                3                 13
  R2                1                 17
  RX                5                 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"
D59V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10P LOSS MUTATED       9                         1
  10P LOSS WILD-TYPE    79                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           0    37
  10P LOSS WILD-TYPE                                         1   206
D59V12, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                                    9                 79
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   37                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"

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    35  18
  10Q LOSS WILD-TYPE 207 104
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                53                311 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                18                104 
$`10Q LOSS MUTATED`
TCGA-BR-4191 TCGA-BR-6458 TCGA-BR-7901 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8365 
       18.35         7.00         0.95         1.32        16.31         2.96 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A4CQ TCGA-CD-5799 
        5.39         9.21        20.22         0.59        22.26         3.25 
TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-A48A TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4455 
        0.07         0.10         0.13         7.99         4.01        12.03 
TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-5730 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6527 
       18.97        22.98         4.01        19.13        18.54         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-EQ-8122 TCGA-FP-7829 TCGA-FP-8631 
       15.22        15.98        12.79         7.79        19.53         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GH 
        1.55         0.23         5.92        14.17        12.10        11.77 
TCGA-HU-A4HD TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR 
       27.42        18.81        18.38         1.41         6.44         6.74 
TCGA-KB-A93H TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       28.90         8.94         5.79        37.74         5.46        13.02 
TCGA-VQ-A8PK TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       17.85        28.70         8.58        40.08         0.79 

$`10Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.12        10.13        13.68        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.16        18.54        12.43         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       17.49         0.82         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 
        0.72         0.26        12.95         0.26         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 
        0.95        13.74         4.31        14.04         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
       19.17        14.79         0.69         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        0.72         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         0.62        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        3.02         0.92        13.41        13.51        12.89         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       11.57         5.13         2.83        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 
        0.10         0.10         0.13         0.13         0.10         6.35 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.13         0.13         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.08        14.01        29.98        47.05        19.07 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 
       21.99         9.01         7.07        12.00        30.97         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 
       12.03        15.02        28.96        79.07        65.10        55.04 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 
       21.07         7.99        12.36        12.66        11.93        20.55 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6818 
       18.84        18.61        17.85         5.95        17.19        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
        0.23         6.97        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 
       11.31        11.44         9.76         2.96        15.65         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.40         7.13         0.62        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 
       72.23        21.27         8.12         0.39         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-HF-A5NB TCGA-HJ-7597 
       17.06        59.54         5.03        13.58        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        1.51        14.27        12.59        11.41        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       22.75        25.81        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        17.69        12.30         9.67         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN 
       21.21         3.45         3.39         5.36         5.19        13.08 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.87         5.56         1.81         2.53         5.56        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DV 
       71.38        57.44        35.61        16.87         0.92        13.25 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       31.10        21.73        22.36        23.77         7.73        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO 
       33.63        46.26        16.31         2.70         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY 
       23.41        15.65        19.30        23.57        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       59.18        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 
        7.36         9.73        44.25         8.61        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        6.58         5.72        29.98        21.11         4.21 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             40.08             122.30 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              8.94              11.70 
[1] "0.1 - 40.1 (8.9)"   "0.1 - 122.3 (11.7)"
[1] "hr=" "1.1"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         0        3        4        3         3        10
  10Q LOSS WILD-TYPE       2       10       35       28        33        39
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           0         15          5          7        3
  10Q LOSS WILD-TYPE         3         62         50         30       34
D60V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 10
  STAGE IB                  4                 35
  STAGE II                  3                 28
  STAGE IIA                 3                 33
  STAGE IIB                10                 39
  STAGE III                 0                  3
  STAGE IIIA               15                 62
  STAGE IIIB                5                 50
  STAGE IIIC                7                 30
  STAGE IV                  3                 34
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED     5  14  24  10
  10Q LOSS WILD-TYPE  16  73 149  94
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                5                 16
  T2               14                 73
  T3               24                149
  T4               10                 94
[1] 4 2
[1] TRUE
[1] "dimension of 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    11  16  13  14
  10Q LOSS WILD-TYPE 111  91  62  65
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               11                111
  N1               16                 91
  N2               13                 62
  N3               14                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  10Q LOSS MUTATED    50   3   4
  10Q LOSS WILD-TYPE 303  21  14
D60V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               50                303
  M1                3                 21
  MX                4                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    20  37
  10Q LOSS WILD-TYPE 131 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     20   37
  10Q LOSS WILD-TYPE  131  207
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               20                131
  MALE                 37                207
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  10Q LOSS MUTATED                                       3
  10Q LOSS WILD-TYPE                                    62
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                       19
  10Q LOSS WILD-TYPE                                                    138
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                                  12
  10Q LOSS WILD-TYPE                                                                57
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  10Q LOSS MUTATED                                                 13
  10Q LOSS WILD-TYPE                                               51
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  10Q LOSS MUTATED                                                          5
  10Q LOSS WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  10Q LOSS MUTATED                                                           1
  10Q LOSS WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  10Q LOSS MUTATED                                          3
  10Q LOSS WILD-TYPE                                        6
D60V8, multiclass
                                                                   clus
vv                                                                  10Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            3
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          19
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  10Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             62
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           138
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 57
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  56
  10Q LOSS WILD-TYPE   5 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   56
  10Q LOSS WILD-TYPE    5  333
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 1                  5
  YES               56                333
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    45   2   3   4
  10Q LOSS WILD-TYPE 273  14  15  21
D60V10, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               45                273
  R1                2                 14
  R2                3                 15
  RX                4                 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"
D60V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  10Q LOSS MUTATED      12                         1
  10Q LOSS WILD-TYPE    76                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           0    37
  10Q LOSS WILD-TYPE                                         1   206
D60V12, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                                   12                 76
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   37                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"

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    33  21
  11P LOSS WILD-TYPE 209 101
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                54                310 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                21                101 
$`11P LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4279 TCGA-BR-6564 TCGA-BR-7723 TCGA-BR-8080 
        6.61         6.97         9.57         0.82        18.54         0.49 
TCGA-BR-8289 TCGA-BR-8297 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-CD-5799 TCGA-CD-5800 
        0.26         7.40         0.92         0.72         3.25        13.15 
TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A48A TCGA-CG-4443 TCGA-CG-4444 
        0.30         0.07         6.35         0.13        29.98        47.05 
TCGA-CG-4460 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5730 TCGA-D7-5578 TCGA-D7-5579 
       21.99        30.97        12.03         4.01        12.66        11.93 
TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-8578 
       20.55        18.54         4.14        15.22        15.98        21.14 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-A72C TCGA-FP-8211 TCGA-HJ-7597 TCGA-HU-8245 
        7.40         0.62         8.12        13.58        26.47        12.59 
TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
       14.17        22.75         2.10        17.69        12.30         9.67 
TCGA-IN-8663 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-RD-A8MW TCGA-VQ-A8DT 
        3.39         5.19         6.44         6.74        37.91        37.74 
TCGA-VQ-A8DV TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 
       13.25        17.85        23.57        44.25         8.61         4.54 

$`11P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62        11.70         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         6.61        34.68        15.95        13.12        10.13 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68         7.00        39.12         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.22        16.14         1.25         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       23.93        15.42        28.01         0.69         0.16        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        0.95         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        1.32         0.69        12.26        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 
       12.95        16.31         1.55         1.48         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 
       13.45         0.20         7.53         0.49        11.54        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T 
       16.44         0.59        15.68         0.62        10.68        12.56 
TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV 
        1.15         0.66         3.02        22.26        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         0.79        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5803 
       13.64        11.57         5.13         2.83        13.18         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.10         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 
        0.10         0.10         0.13         0.13         0.10         0.13 
TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.07         0.10         0.10         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 
       20.02         3.02        27.02        15.95         1.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4449 TCGA-CG-4455 
        8.05        54.08         4.01        14.01        19.07        12.03 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
        9.01        18.97         7.07        12.00        22.98         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 
       15.02        28.96        79.07        65.10        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
        7.99        12.36        19.13        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        5.95        17.19        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 
       24.72        16.80        19.50        17.19         0.23         6.97 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ 
       14.76        13.71        11.24        11.31        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO 
        2.96        15.65         4.34         7.13         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 
        6.58        14.47        72.23        21.27         0.39        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
        3.02        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        1.55         0.23        18.08         1.51         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH 
       12.30        11.84        24.20         3.25        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU 
       21.37        29.98         8.98         0.10         6.51         6.25 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB 
       10.19         0.26        12.95        19.36         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-A6RI TCGA-IN-A6RJ 
       27.42        21.21         3.45        18.81        18.38         5.36 
TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
       13.08         1.41         6.87         5.56         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        5.56        60.56        28.90         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 
       11.05         8.61         4.67        16.67       122.30        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      115.69       116.38        71.38        57.44         8.94        35.61 
TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 
       16.87         5.79         0.92         5.46        13.02        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26        16.31         2.70         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A 
       15.65        19.30        64.57        14.33        59.18        28.70 
TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W 
       11.70         8.68        49.25        20.81         1.71         7.36 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 
        8.58         9.73        55.43         6.58         5.72        40.08 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        21.11         4.21         0.79 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             47.05             122.30 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            10.800             11.635 
[1] "0.1 - 47.0 (10.8)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.3"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         0        1        6        6         4         5
  11P LOSS WILD-TYPE       2       12       33       25        32        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           0         16          5          5        6
  11P LOSS WILD-TYPE         3         61         50         32       31
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 12
  STAGE IB                  6                 33
  STAGE II                  6                 25
  STAGE IIA                 4                 32
  STAGE IIB                 5                 44
  STAGE III                 0                  3
  STAGE IIIA               16                 61
  STAGE IIIB                5                 50
  STAGE IIIC                5                 32
  STAGE IV                  6                 31
[1] 11  2
[1] TRUE
[1] "dimension of 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     2  19  24  10
  11P LOSS WILD-TYPE  19  68 149  94
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                2                 19
  T2               19                 68
  T3               24                149
  T4               10                 94
[1] 4 2
[1] TRUE
[1] "dimension of 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    13  17  13  11
  11P LOSS WILD-TYPE 109  90  62  68
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               13                109
  N1               17                 90
  N2               13                 62
  N3               11                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  11P LOSS MUTATED    47   5   3
  11P LOSS WILD-TYPE 306  19  15
D61V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               47                306
  M1                5                 19
  MX                3                 15
[1] 3 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    18  37
  11P LOSS WILD-TYPE 133 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     18   37
  11P LOSS WILD-TYPE  133  207
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               18                133
  MALE                 37                207
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11P LOSS MUTATED                                       7
  11P LOSS WILD-TYPE                                    58
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                       16
  11P LOSS WILD-TYPE                                                    141
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                                  12
  11P LOSS WILD-TYPE                                                                57
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  11P LOSS MUTATED                                                 13
  11P LOSS WILD-TYPE                                               51
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11P LOSS MUTATED                                                          2
  11P LOSS WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  11P LOSS MUTATED                                                           4
  11P LOSS WILD-TYPE                                                         4
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11P LOSS MUTATED                                          1
  11P LOSS WILD-TYPE                                        8
D61V8, multiclass
                                                                   clus
vv                                                                  11P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               12
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  11P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 57
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  55
  11P LOSS WILD-TYPE   6 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   55
  11P LOSS WILD-TYPE    6  334
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 0                  6
  YES               55                334
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    40   2   5   4
  11P LOSS WILD-TYPE 278  14  13  21
D61V10, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               40                278
  R1                2                 14
  R2                5                 13
  RX                4                 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"
D61V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11P LOSS MUTATED      15                         0
  11P LOSS WILD-TYPE    73                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           0    32
  11P LOSS WILD-TYPE                                         1   211
D61V12, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   32                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"

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    30  20
  11Q LOSS WILD-TYPE 212 102
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                50                314 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                20                102 
$`11Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4279 TCGA-BR-6709 TCGA-BR-7723 TCGA-BR-8080 
        6.61         6.97         9.57         1.25        18.54         0.49 
TCGA-BR-8289 TCGA-BR-8365 TCGA-BR-8486 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        0.26         2.96        20.22        22.26         0.92         0.72 
TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8527 
       13.51         1.15         3.25        13.15         0.30         0.07 
TCGA-CD-A48A TCGA-CG-4437 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-5724 TCGA-D7-5578 
        0.13         8.05        29.98        12.03        12.03        12.66 
TCGA-D7-5579 TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-A74A TCGA-EQ-5647 
       11.93        18.54         4.14        15.98         7.40         0.62 
TCGA-FP-7916 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-8610 
        3.02        13.58         0.23        26.47        14.17         0.76 
TCGA-HU-A4GD TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-IN-A6RL TCGA-IN-A6RP 
       22.75         2.10        17.69         9.67         5.19         6.44 
TCGA-RD-A8MW TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91Q 
       37.91        37.74        13.25        17.85        23.57        20.81 
TCGA-VQ-A91Z TCGA-VQ-A922 
       44.25         8.61 

$`11Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62        11.70         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        6.18         6.61        34.68        15.95        13.12        10.13 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68         7.00        39.12         0.82         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 
       13.84        13.22        16.14         8.98        21.11        30.90 
TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 
       31.20        32.94        12.82         9.21        24.76        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       23.93        15.42        28.01         0.69         0.16        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
        0.95         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        1.32         0.69        12.26        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 
       19.50         0.36         0.26        22.19         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U 
        0.59        15.68         0.62        10.68        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.66         3.02        13.41        13.51        12.89         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       14.17         0.53        12.82         0.66        19.36         0.46 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.65        20.42        13.64        11.57         5.13         2.83 
TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 
       13.18         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MG 
        0.10         6.35         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.10         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         7.99        54.08         4.01        14.01 
TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       47.05        19.07        21.99         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        15.02        28.96 
TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 
       79.07        65.10         4.01        55.04        21.07         7.99 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 
       12.36        19.13        20.55        18.84        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
        5.95        17.19        15.22        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
        6.97        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B 
       11.44         9.76         2.96        15.65         4.34         7.13 
TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        7.79        16.24         6.58        14.47        72.23        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        8.12         0.39        19.53        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 
        5.03         0.56         1.55        18.08         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G2 
       14.27        12.59        11.41        12.10        10.62        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF 
        5.59        12.30        11.84        24.20         3.25        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 
        6.25        10.19         0.26        12.95        19.36        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        8.88         8.81        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR 
        3.39        18.38         5.36        13.08         1.41         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.87         5.56         1.81         2.53         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT 
       28.90         3.72        19.73         4.31        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
        4.67        16.67       122.30        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        0.92         5.46        13.02        31.10        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       23.77         7.73        19.07        33.63        46.26        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
        2.70         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A924 
       49.25         1.71         7.36         8.58         9.73        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        4.54         6.58         5.72        40.08        29.98        21.11 
TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        4.21         0.79 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.07               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             44.25             122.30 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              9.62              11.70 
[1] "0.1 - 44.2 (9.6)"   "0.1 - 122.3 (11.7)"
[1] "hr=" "1.4"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         0        3        2        8         2         4
  11Q LOSS WILD-TYPE       2       10       37       23        34        45
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           0         13          7          6        5
  11Q LOSS WILD-TYPE         3         64         48         31       32
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 10
  STAGE IB                  2                 37
  STAGE II                  8                 23
  STAGE IIA                 2                 34
  STAGE IIB                 4                 45
  STAGE III                 0                  3
  STAGE IIIA               13                 64
  STAGE IIIB                7                 48
  STAGE IIIC                6                 31
  STAGE IV                  5                 32
[1] 11  2
[1] TRUE
[1] "dimension of 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     4  13  22  12
  11Q LOSS WILD-TYPE  17  74 151  92
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                4                 17
  T2               13                 74
  T3               22                151
  T4               12                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q LOSS MUTATED     9  16  10  15
  11Q LOSS WILD-TYPE 113  91  65  64
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                9                113
  N1               16                 91
  N2               10                 65
  N3               15                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  11Q LOSS MUTATED    43   3   5
  11Q LOSS WILD-TYPE 310  21  13
D62V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               43                310
  M1                3                 21
  MX                5                 13
[1] 3 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    16  35
  11Q LOSS WILD-TYPE 135 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     16   35
  11Q LOSS WILD-TYPE  135  209
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               16                135
  MALE                 35                209
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  11Q LOSS MUTATED                                       4
  11Q LOSS WILD-TYPE                                    61
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                       18
  11Q LOSS WILD-TYPE                                                    139
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                                   9
  11Q LOSS WILD-TYPE                                                                60
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  11Q LOSS MUTATED                                                 13
  11Q LOSS WILD-TYPE                                               51
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  11Q LOSS MUTATED                                                          3
  11Q LOSS WILD-TYPE                                                       18
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  11Q LOSS MUTATED                                                           2
  11Q LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  11Q LOSS MUTATED                                          2
  11Q LOSS WILD-TYPE                                        7
D62V8, multiclass
                                                                   clus
vv                                                                  11Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            4
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                9
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  11Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             61
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 60
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  51
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     0  51
  11Q LOSS WILD-TYPE   6 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0   51
  11Q LOSS WILD-TYPE    6  338
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 0                  6
  YES               51                338
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    38   3   2   4
  11Q LOSS WILD-TYPE 280  13  16  21
D62V10, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               38                280
  R1                3                 13
  R2                2                 16
  RX                4                 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"
D62V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  11Q LOSS MUTATED      13                         0
  11Q LOSS WILD-TYPE    75                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           0    31
  11Q LOSS WILD-TYPE                                         1   212
D62V12, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                                   13                 75
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   31                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"

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    30  19
  12P LOSS WILD-TYPE 212 103
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                49                315 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                19                103 
$`12P LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7901 
        6.61         6.18        10.13        35.24        15.42         0.95 
TCGA-BR-8060 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4J6 
        1.32         5.39         9.21         0.59         0.62         0.66 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 
       13.15         0.30         0.07         0.13         6.35         0.13 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4477 TCGA-CG-5725 
        0.10        20.02         7.99        29.98        30.97        15.02 
TCGA-CG-5732 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A4YT TCGA-EQ-5647 TCGA-EQ-8122 
       55.04        15.22        12.33        14.27         0.62         7.79 
TCGA-F1-6875 TCGA-FP-8631 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-HU-A4H4 
       72.23         0.56        12.59        11.77        12.95        17.69 
TCGA-HU-A4H5 TCGA-IN-A6RL TCGA-IN-A6RN TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8PJ 
       12.30         5.19        13.08         5.46        13.02         2.70 
TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-AA68 
       23.57        14.33         8.58        44.25         4.54        40.08 
TCGA-ZQ-A9CR 
        0.79 

$`12P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         9.57         6.61        34.68        15.95        13.12 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 
       13.68         7.00        39.12         0.82         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       23.93        28.01         0.69         0.16        18.54        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 
        0.69        12.76        18.71        17.49         0.82         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 
       12.26         0.49        20.55         0.72         0.26        12.95 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.26        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       14.79         0.69         0.26        15.85         3.72         0.72 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68        10.68        12.56         1.15         0.66         3.02 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         0.92        13.41        13.51        12.89         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53        12.82        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 
        5.13         2.83         3.25        13.18         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         0.13         0.10         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.07         0.10         0.10         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 
        1.02         8.05        54.08         4.01        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 
       19.07        12.03        21.99         9.01        18.97         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       12.00        22.98         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        12.03        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 
       17.85         5.95        17.19         4.14        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       10.55        11.31        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV 
        0.23         6.97        21.14        20.91        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       11.44         9.76         2.96        15.65         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C 
        7.13        16.24         6.58        14.47        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39        19.53         3.02        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         1.55         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        1.51         5.92        14.27        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD 
        2.10        19.36         9.67         8.88         8.81        27.42 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ 
       21.21         3.45        18.81         3.39        18.38         5.36 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU 
        1.41         6.44         6.74         6.87         5.56         1.81 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        2.53         5.56        60.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.31        11.05         8.61         4.67        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 
       13.25        31.10        21.73        22.36        23.77         7.73 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM 
       19.07        33.63        46.26        16.31        17.85         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ 
        9.27        23.41        15.65        19.30        64.57        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       28.70        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        7.36         9.73         8.61        55.43         6.58         5.72 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
       29.98        21.11         4.21 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.07               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             72.23             122.30 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              9.21              11.70 
[1] "0.1 - 72.2 (9.2)"   "0.1 - 122.3 (11.7)"
[1] "hr=" "1.3"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         0        3        8        4         6         5
  12P LOSS WILD-TYPE       2       10       31       27        30        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           0         11          5          6        4
  12P LOSS WILD-TYPE         3         66         50         31       33
D63V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 10
  STAGE IB                  8                 31
  STAGE II                  4                 27
  STAGE IIA                 6                 30
  STAGE IIB                 5                 44
  STAGE III                 0                  3
  STAGE IIIA               11                 66
  STAGE IIIB                5                 50
  STAGE IIIC                6                 31
  STAGE IV                  4                 33
[1] 11  2
[1] TRUE
[1] "dimension of 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     3  15  24  10
  12P LOSS WILD-TYPE  18  72 149  94
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                3                 18
  T2               15                 72
  T3               24                149
  T4               10                 94
[1] 4 2
[1] TRUE
[1] "dimension of 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    20  10  12  10
  12P LOSS WILD-TYPE 102  97  63  69
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               20                102
  N1               10                 97
  N2               12                 63
  N3               10                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  12P LOSS MUTATED    47   3   4
  12P LOSS WILD-TYPE 306  21  14
D63V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0               47                306
  M1                3                 21
  MX                4                 14
[1] 3 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    25  29
  12P LOSS WILD-TYPE 126 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     25   29
  12P LOSS WILD-TYPE  126  215
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               25                126
  MALE                 29                215
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12P LOSS MUTATED                                       2
  12P LOSS WILD-TYPE                                    63
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                       23
  12P LOSS WILD-TYPE                                                    134
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                                  10
  12P LOSS WILD-TYPE                                                                59
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  12P LOSS MUTATED                                                 15
  12P LOSS WILD-TYPE                                               49
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12P LOSS MUTATED                                                          0
  12P LOSS WILD-TYPE                                                       21
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  12P LOSS MUTATED                                                           3
  12P LOSS WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12P LOSS MUTATED                                          1
  12P LOSS WILD-TYPE                                        8
D63V8, multiclass
                                                                   clus
vv                                                                  12P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          23
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               10
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                15
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  12P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           134
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 59
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  49
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  53
  12P LOSS WILD-TYPE   5 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   53
  12P LOSS WILD-TYPE    5  336
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 1                  5
  YES               53                336
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    39   1   4   5
  12P LOSS WILD-TYPE 279  15  14  20
D63V10, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               39                279
  R1                1                 15
  R2                4                 14
  RX                5                 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"
D63V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12P LOSS MUTATED      13                         2
  12P LOSS WILD-TYPE    75                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           0    30
  12P LOSS WILD-TYPE                                         1   213
D63V12, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                                   13                 75
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   30                213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    23  15
  12Q LOSS WILD-TYPE 219 107
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                38                326 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                107 
$`12Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7901 TCGA-BR-8060 
        6.61        10.13        35.24        15.42         0.95         1.32 
TCGA-BR-8286 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A4J6 
       12.95         5.39         9.21         0.59         0.62         0.66 
TCGA-CD-5802 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
        0.30         6.35         0.13         0.10        20.02         7.99 
TCGA-CG-4443 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6528 TCGA-D7-A6F2 TCGA-EQ-5647 
       29.98        15.02        55.04        15.22        15.65         0.62 
TCGA-EQ-8122 TCGA-FP-8211 TCGA-FP-8631 TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-IN-A6RP 
        7.79        13.58         0.56        11.77        12.95         6.44 
TCGA-KB-A93H TCGA-VQ-A8DU TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A91Z TCGA-VQ-A925 
       28.90         5.46        17.85        23.57        44.25         4.54 
TCGA-VQ-AA68 TCGA-ZQ-A9CR 
       40.08         0.79 

$`12Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6565 
       13.12        13.68         7.00        39.12         0.82         0.62 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        23.93        28.01         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.69        12.76        18.71        17.49         0.82 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
        0.26        16.31         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8484 
       14.79         0.69         0.26        15.85         3.72         0.72 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68        10.68        12.56         1.15         0.66         3.02 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
       22.26         0.92        13.41        13.51        12.89         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 
        0.72        14.17         0.53        12.82        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
        0.46        20.65        20.42         1.15        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5803 
        5.13         2.83         3.25        13.15        13.18         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 
        0.07         0.07         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.13         0.13         0.13         0.07         0.10         0.10 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 
        4.01        14.01        47.05        19.07        12.03        21.99 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
        9.01        18.97         7.07        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 
       21.07         7.99        12.36        12.66        11.93        19.13 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       20.55        18.84        18.54        18.61        17.85         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 
       17.19         4.14        15.98        12.79        10.55        11.31 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       12.33        24.72        16.80        19.50        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
        6.97        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EX 
       15.16        13.78        14.76        13.71        11.24        11.31 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.44         9.76         2.96         4.34         7.40         7.13 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C 
       16.24         6.58        14.47        72.23        21.27         8.12 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 
        0.39        19.53         3.02        22.29        17.06        59.54 
TCGA-FP-8210 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 
        5.03         1.55         0.23        18.08        26.47         1.51 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 
        5.92        14.27        12.59        14.17        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        22.75        25.81        21.37        29.98 
TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
        8.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 
        2.10        19.36        17.69        12.30         9.67         8.88 
TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.81        27.42        21.21         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RR 
       18.38         5.36         5.19        13.08         1.41         6.74 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 
        6.87         5.56         1.81         2.53         5.56        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        37.74        13.25        13.02        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       22.36        23.77         7.73        19.07        33.63        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.70         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D 
       19.30        64.57        14.33        59.18        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X 
        8.68        49.25        20.81         1.71         7.36         8.58 
TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B 
        9.73         8.61        55.43         6.58         5.72        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 
       21.11         4.21 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.10               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             55.04             122.30 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              8.60              11.77 
[1] "0.1 - 55.0 (8.6)"   "0.1 - 122.3 (11.8)"
[1] "hr=" "1.4"
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         0        2        5        3         6         6
  12Q LOSS WILD-TYPE       2       11       34       28        30        43
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0          7          4          6        2
  12Q LOSS WILD-TYPE         3         70         51         31       35
D64V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 11
  STAGE IB                  5                 34
  STAGE II                  3                 28
  STAGE IIA                 6                 30
  STAGE IIB                 6                 43
  STAGE III                 0                  3
  STAGE IIIA                7                 70
  STAGE IIIB                4                 51
  STAGE IIIC                6                 31
  STAGE IV                  2                 35
[1] 11  2
[1] TRUE
[1] "dimension of 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     3   7  23   8
  12Q LOSS WILD-TYPE  18  80 150  96
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                3                 18
  T2                7                 80
  T3               23                150
  T4                8                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q LOSS MUTATED    16   8   8   9
  12Q LOSS WILD-TYPE 106  99  67  70
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               16                106
  N1                8                 99
  N2                8                 67
  N3                9                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  12Q LOSS MUTATED    37   1   5
  12Q LOSS WILD-TYPE 316  23  13
D64V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0               37                316
  M1                1                 23
  MX                5                 13
[1] 3 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    19  24
  12Q LOSS WILD-TYPE 132 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     19   24
  12Q LOSS WILD-TYPE  132  220
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               19                132
  MALE                 24                220
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  12Q LOSS MUTATED                                       2
  12Q LOSS WILD-TYPE                                    63
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                       21
  12Q LOSS WILD-TYPE                                                    136
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                                   8
  12Q LOSS WILD-TYPE                                                                61
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  12Q LOSS MUTATED                                                 12
  12Q LOSS WILD-TYPE                                               52
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  12Q LOSS MUTATED                                                          0
  12Q LOSS WILD-TYPE                                                       21
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  12Q LOSS MUTATED                                                           0
  12Q LOSS WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  12Q LOSS MUTATED                                          0
  12Q LOSS WILD-TYPE                                        9
D64V8, multiclass
                                                                   clus
vv                                                                  12Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          21
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                8
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         0
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  12Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           136
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 61
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  52
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          21
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  42
  12Q LOSS WILD-TYPE   5 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   42
  12Q LOSS WILD-TYPE    5  347
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 1                  5
  YES               42                347
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    31   2   2   3
  12Q LOSS WILD-TYPE 287  14  16  22
D64V10, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               31                287
  R1                2                 14
  R2                2                 16
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  12Q LOSS MUTATED       8                         0
  12Q LOSS WILD-TYPE    80                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0    28
  12Q LOSS WILD-TYPE                                         1   215
D64V12, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                                    8                 80
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   28                215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    17  14
  13Q LOSS WILD-TYPE 225 108
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                31                333 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                108 
$`13Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7716 
        6.61         6.97        10.13         0.82         1.25        28.01 
TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A4IY TCGA-CD-8526 
        7.40        19.50        20.22         0.59        12.89         0.07 
TCGA-CD-8533 TCGA-CG-4301 TCGA-CG-4466 TCGA-CG-4475 TCGA-D7-6525 TCGA-D7-8575 
        0.13         3.02        18.97        22.98         5.95         0.23 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-FP-7916 TCGA-FP-8211 TCGA-HU-A4GC TCGA-HU-A4H2 
       21.14        16.44         3.02        13.58         3.25        12.95 
TCGA-IN-A6RJ TCGA-IN-A6RR TCGA-RD-A7BS TCGA-VQ-A8P5 TCGA-VQ-A8PM TCGA-VQ-A91Z 
        5.36         6.74        11.05         7.73         1.87        44.25 
TCGA-VQ-A925 
        4.54 

$`13Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62        11.70         4.64         7.43        18.35        30.90 
TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
        6.18         9.57         6.61        34.68        15.95        13.12 
TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.68         7.00        39.12         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       13.22        16.14         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 
       32.94        12.82         9.21        24.76        35.24        23.93 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 
       15.42         0.69         0.16        18.54        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        0.69        12.76        18.71        17.49         0.82         1.32 
TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.69        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 
       12.95         0.26        16.31         1.55         1.48         6.18 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 
        4.31        14.04         3.32         0.36        19.17        14.79 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
        9.21         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         0.62        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
        3.02        22.26         0.92        13.41        13.51         0.79 
TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.72        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
        0.30         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG 
        6.35         0.13         0.13         0.13         0.13         0.07 
TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4304 TCGA-CG-4305 
        0.10         0.10         0.10        20.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
        1.02         7.99         8.05        54.08         4.01        14.01 
TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 
       29.98        47.05        19.07        12.03        21.99         9.01 
TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
        7.07        12.00        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 
        0.99         6.02         0.99       105.07        12.03        15.02 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 
       28.96        79.07        65.10         4.01        55.04        21.07 
TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 
        7.99        12.36        12.66        11.93        19.13        20.55 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 TCGA-D7-6527 
       18.84        18.54        18.61        17.85        17.19         4.14 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 
       24.72        16.80        19.50        17.19         6.97        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
       11.24        11.31        11.44         9.76         2.96        15.65 
TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO 
        4.34         7.40         7.13         0.62         7.79        16.24 
TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        6.58        14.47        72.23        21.27         8.12         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 
       19.53        22.29        17.06        59.54         5.03         0.56 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 
        1.55         0.23        18.08        26.47         1.51         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       14.27        12.59        14.17        11.41        12.10        10.62 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        12.30        11.84        24.20 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP 
       22.75        25.81        11.77        21.37        29.98         8.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
        0.10         6.51         6.25        10.19         0.26         2.10 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        17.69        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       27.42        21.21         3.45        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS TCGA-IN-A7NT 
        5.19        13.08         1.41         6.44         6.87         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG 
        1.81         2.53         5.56        60.56        28.90         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
       19.73         4.31         8.61         4.67        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        5.46        13.25        13.02        31.10        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ 
       23.77        19.07        33.63        46.26        16.31         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
       17.85         9.27        23.41        15.65        19.30        23.57 
TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       64.57        14.33        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       49.25        20.81         1.71         7.36         8.58         9.73 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B 
        8.61        55.43         6.58         5.72        40.08        29.98 
TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       21.11         4.21         0.79 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             44.25             122.30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              6.97              11.93 
[1] "0.1 - 44.2 (7.0)"   "0.1 - 122.3 (11.9)"
[1] "hr=" "1.7"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         0        1        4        1         1         5
  13Q LOSS WILD-TYPE       2       12       35       30        35        44
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           0         11          5          3        3
  13Q LOSS WILD-TYPE         3         66         50         34       34
D65V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 12
  STAGE IB                  4                 35
  STAGE II                  1                 30
  STAGE IIA                 1                 35
  STAGE IIB                 5                 44
  STAGE III                 0                  3
  STAGE IIIA               11                 66
  STAGE IIIB                5                 50
  STAGE IIIC                3                 34
  STAGE IV                  3                 34
[1] 11  2
[1] TRUE
[1] "dimension of 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     2   6  19   8
  13Q LOSS WILD-TYPE  19  81 154  96
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                2                 19
  T2                6                 81
  T3               19                154
  T4                8                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q LOSS MUTATED     8  12   7   7
  13Q LOSS WILD-TYPE 114  95  68  72
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                8                114
  N1               12                 95
  N2                7                 68
  N3                7                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  13Q LOSS MUTATED    30   1   4
  13Q LOSS WILD-TYPE 323  23  14
D65V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               30                323
  M1                1                 23
  MX                4                 14
[1] 3 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    15  20
  13Q LOSS WILD-TYPE 136 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     15   20
  13Q LOSS WILD-TYPE  136  224
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               15                136
  MALE                 20                224
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  13Q LOSS MUTATED                                       6
  13Q LOSS WILD-TYPE                                    59
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                       16
  13Q LOSS WILD-TYPE                                                    141
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                                   3
  13Q LOSS WILD-TYPE                                                                66
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  13Q LOSS MUTATED                                                  7
  13Q LOSS WILD-TYPE                                               57
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  13Q LOSS MUTATED                                                          1
  13Q LOSS WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  13Q LOSS MUTATED                                                           0
  13Q LOSS WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  13Q LOSS MUTATED                                          1
  13Q LOSS WILD-TYPE                                        8
D65V8, multiclass
                                                                   clus
vv                                                                  13Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          16
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                3
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 7
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         1
                                                                   clus
vv                                                                  13Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           141
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 66
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  57
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     2  33
  13Q LOSS WILD-TYPE   4 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   33
  13Q LOSS WILD-TYPE    4  356
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 2                  4
  YES               33                356
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    25   3   2   4
  13Q LOSS WILD-TYPE 293  13  16  21
D65V10, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               25                293
  R1                3                 13
  R2                2                 16
  RX                4                 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"
D65V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  13Q LOSS MUTATED       7                         0
  13Q LOSS WILD-TYPE    81                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           0    23
  13Q LOSS WILD-TYPE                                         1   220
D65V12, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                                    7                 81
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   23                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    63  30
  14Q LOSS WILD-TYPE 179  92
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                93                271 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                30                 92 
$`14Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-4279 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6709 
        6.61         9.57         7.00         0.82         0.62         1.25 
TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7959 
       31.20        35.24        15.42        28.01        18.54        18.71 
TCGA-BR-8058 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 TCGA-BR-8381 TCGA-BR-8483 
       17.49        12.95         0.26        14.79         0.26         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A4CS TCGA-BR-A4J1 
        0.72         9.21        11.54        15.68         0.92         0.72 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5801 
        0.66        19.36         0.46        20.65         1.15        13.18 
TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8527 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A489 
        0.07         0.07         0.07         0.13         0.13         0.13 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4477 
        0.10        20.02         7.99         8.05        54.08        30.97 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 
       20.55        18.84        18.54        17.19         4.14        15.98 
TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A TCGA-EQ-8122 
        6.97        16.44        11.31         2.96         7.40         7.79 
TCGA-F1-A72C TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-HJ-7597 TCGA-HU-8245 
        8.12         3.02        17.06         0.56        26.47        12.59 
TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4H0 TCGA-HU-A4H4 
       14.17         3.25        11.77         8.98         2.10        17.69 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU 
       27.42        21.21         5.19         6.44         6.74         1.81 
TCGA-IP-7968 TCGA-KB-A93H TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 
        2.53        28.90        16.67        37.91       115.69         8.94 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ 
        5.46        13.02        31.10         7.73        46.26         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91Q 
       17.85        23.57        64.57        14.33        59.18        20.81 
TCGA-VQ-A91Z TCGA-VQ-AA6B TCGA-ZQ-A9CR 
       44.25        29.98         0.79 

$`14Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         6.18         6.61        34.68        15.95        13.12 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 
       10.13        13.68        39.12        32.78        13.84        13.22 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 
       16.14         8.98        21.11        30.90        32.94        12.82 
TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
        9.21        24.76        23.93         0.69         0.16        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        0.95         0.69        12.76         0.82         1.32         0.69 
TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 
       12.26         0.49        20.55         0.72         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        1.55         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 
        0.26        22.19         2.96         0.95        13.74         4.31 
TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8382 
       14.04         3.32         0.36        19.17         0.69        15.85 
TCGA-BR-8384 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        3.72        20.22         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 
       13.45         0.20         7.53         0.49        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        0.59         0.62        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        3.02        22.26        13.41        13.51        12.89         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J8 TCGA-BR-A4PE TCGA-BR-A4QI 
       14.17         0.53        12.82        13.51        20.42        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 
       11.57         5.13         2.83         3.25        13.15         0.30 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 
        0.07         0.07         0.10         0.13         0.16         0.10 
TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C 
        0.10         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
        0.07         0.10         0.10         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        1.02         4.01        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       12.03        21.99         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       22.98         6.97         1.02         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       12.66        11.93        19.13        18.61        17.85         5.95 
TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 
       15.22        12.79        10.55        11.31        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19         0.23        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       14.27         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74B 
       11.24        11.44         9.76        15.65         4.34         7.13 
TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 
        0.62        16.24         6.58        14.47        72.23        21.27 
TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 
        0.39        19.53        22.29        59.54         5.03        13.58 
TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        1.55         0.23        18.08         1.51         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       12.30        11.84        24.20        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       12.95        19.36        12.30         9.67         8.88         8.81 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-MX-A5UG 
        1.41         6.87         5.56         5.56        60.56         3.72 
TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
       19.73         4.31        11.05         8.61         4.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        5.79         0.92        37.74        13.25        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PO 
       23.77        19.07        33.63        16.31         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       23.41        15.65        19.30        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 
       49.25         1.71         7.36         8.58         9.73         8.61 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J 
       55.43         4.54         6.58         5.72        40.08        21.11 
TCGA-ZA-A8F6 
        4.21 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            115.69             122.30 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             11.31              11.70 
[1] "0.1 - 115.7 (11.3)" "0.1 - 122.3 (11.7)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         0        2        7       11        11        11
  14Q LOSS WILD-TYPE       2       11       32       20        25        38
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           0         25         17          7        5
  14Q LOSS WILD-TYPE         3         52         38         30       32
D66V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  2                 11
  STAGE IB                  7                 32
  STAGE II                 11                 20
  STAGE IIA                11                 25
  STAGE IIB                11                 38
  STAGE III                 0                  3
  STAGE IIIA               25                 52
  STAGE IIIB               17                 38
  STAGE IIIC                7                 30
  STAGE IV                  5                 32
[1] 11  2
[1] TRUE
[1] "dimension of 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     3  19  53  21
  14Q LOSS WILD-TYPE  18  68 120  83
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                3                 18
  T2               19                 68
  T3               53                120
  T4               21                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  14Q LOSS MUTATED   28 27 26 15
  14Q LOSS WILD-TYPE 94 80 49 64
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               28                 94
  N1               27                 80
  N2               26                 49
  N3               15                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  14Q LOSS MUTATED    89   3   8
  14Q LOSS WILD-TYPE 264  21  10
D66V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               89                264
  M1                3                 21
  MX                8                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    38  62
  14Q LOSS WILD-TYPE 113 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     38   62
  14Q LOSS WILD-TYPE  113  182
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               38                113
  MALE                 62                182
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  14Q LOSS MUTATED                                      13
  14Q LOSS WILD-TYPE                                    52
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                       39
  14Q LOSS WILD-TYPE                                                    118
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                                  20
  14Q LOSS WILD-TYPE                                                                49
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  14Q LOSS MUTATED                                                 20
  14Q LOSS WILD-TYPE                                               44
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  14Q LOSS MUTATED                                                          2
  14Q LOSS WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  14Q LOSS MUTATED                                                           2
  14Q LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  14Q LOSS MUTATED                                          4
  14Q LOSS WILD-TYPE                                        5
D66V8, multiclass
                                                                   clus
vv                                                                  14Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          39
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               20
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         4
                                                                   clus
vv                                                                  14Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           118
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 49
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  99
  14Q LOSS WILD-TYPE   5 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   99
  14Q LOSS WILD-TYPE    5  290
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 1                  5
  YES               99                290
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    84   2   2   7
  14Q LOSS WILD-TYPE 234  14  16  18
D66V10, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               84                234
  R1                2                 14
  R2                2                 16
  RX                7                 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"
D66V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  14Q LOSS MUTATED      24                         1
  14Q LOSS WILD-TYPE    64                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           0    66
  14Q LOSS WILD-TYPE                                         1   177
D66V12, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                                   24                 64
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   66                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"

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    56  21
  15Q LOSS WILD-TYPE 186 101
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                77                287 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                101 
$`15Q LOSS MUTATED`
TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8373 
       35.24        18.54         0.95        12.95         0.26        14.79 
TCGA-BR-8483 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QI 
        5.39        15.68        10.68         0.72        20.65        13.64 
TCGA-CD-5801 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 TCGA-CD-8535 TCGA-CD-A48A 
       13.18         0.07         0.07         0.16         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4440 TCGA-CG-4466 
        0.13         0.10        20.02         7.99         4.01        18.97 
TCGA-CG-5719 TCGA-CG-5724 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6526 
        1.02        12.03        12.66        19.13        20.55        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8576 TCGA-D7-A4YU TCGA-D7-A6EX 
        4.14        15.22        12.79         6.97        16.44        11.31 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-FP-7998 TCGA-FP-A4BF 
        2.96        15.65         7.40         7.79        22.29         1.55 
TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD 
        0.23        26.47        12.59        14.17        12.10        22.75 
TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H6 
        8.98         6.25         2.10        12.95        17.69         9.67 
TCGA-HU-A4HD TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RP TCGA-IN-A7NU TCGA-IP-7968 
       27.42         5.36         5.19         6.44         1.81         2.53 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N9 
        4.31        11.05        16.67        37.91       115.69        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PU TCGA-VQ-A8PZ TCGA-VQ-A91U 
        5.79        37.74         5.46        23.57        59.18         1.71 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6B 
        8.58         9.73         8.61        40.08        29.98 

$`15Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 
       15.95        13.12        10.13        13.68         7.00        39.12 
TCGA-BR-6564 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
        0.82         0.62        32.78        13.84        13.22        16.14 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 
        1.25         8.98        21.11        30.90        31.20        32.94 
TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 
       12.82         9.21        24.76        23.93        15.42        28.01 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
        0.69         0.16        12.43         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49         0.82         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 
       20.55         0.72         0.26        16.31         1.55         1.48 
TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
        7.40         6.18        19.50         0.36         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        0.36        19.17         0.69         0.26        15.85         3.72 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        0.72         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 
        2.14        13.45         0.20         7.53         0.49        11.54 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       15.81        16.44         0.59         0.62        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV 
        0.66         3.02        22.26         0.92        13.41        13.51 
TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
       12.89         0.79        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL 
       19.36        13.51         0.46        20.42         1.15        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 
        5.13         2.83         3.25        13.15         0.30         0.07 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 
        0.07         0.07         0.10         0.13         0.10         0.10 
TCGA-CD-8533 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG 
        0.13         0.10         6.35         0.13         0.13         0.07 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10         0.10         3.02        27.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.08        14.01        29.98        47.05        19.07 
TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       12.03        21.99         9.01         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
       30.97         6.97         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6520 
       55.04        21.07         7.99        12.36        11.93        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-6818 
       18.54        18.61        17.85         5.95        15.98        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 
       11.31        12.33        24.72        16.80        19.50        17.19 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
        0.23        21.14        20.91        14.27         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        4.34         7.13         0.62        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27         8.12         0.39        19.53         3.02 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-HF-A5NB 
       17.06        59.54         5.03        13.58         0.56        18.08 
TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 
        1.51         5.92        14.27        11.41        10.62         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC 
       24.30         5.59        12.30        11.84        24.20         3.25 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT 
       25.81        11.77        21.37        29.98         0.10         6.51 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB 
       10.19         0.26        19.36        12.30         8.88         8.81 
TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RN 
       21.21         3.45        18.81         3.39        18.38        13.08 
TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 
        1.41         6.74         6.87         5.56         5.56        60.56 
TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV 
       28.90         3.72        19.73         8.61         4.67       122.30 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44         8.94        16.87 
TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        0.92        13.25        13.02        31.10        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD 
       23.77         7.73        19.07        33.63        46.26        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
        2.70        17.85         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       19.30        64.57        14.33        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A924 TCGA-VQ-A925 
       49.25        20.81         7.36        44.25        55.43         4.54 
TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        6.58         5.72        21.11         4.21         0.79 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.07               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            115.69             122.30 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             11.05              11.70 
[1] "0.1 - 115.7 (11.1)" "0.1 - 122.3 (11.7)"
[1] "hr=" "1.2"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         0        0        9        7         8         7
  15Q LOSS WILD-TYPE       2       13       30       24        28        42
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           0         23         14          8        5
  15Q LOSS WILD-TYPE         3         54         41         29       32
D67V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 13
  STAGE IB                  9                 30
  STAGE II                  7                 24
  STAGE IIA                 8                 28
  STAGE IIB                 7                 42
  STAGE III                 0                  3
  STAGE IIIA               23                 54
  STAGE IIIB               14                 41
  STAGE IIIC                8                 29
  STAGE IV                  5                 32
[1] 11  2
[1] TRUE
[1] "dimension of 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     2  18  48  14
  15Q LOSS WILD-TYPE  19  69 125  90
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                2                 19
  T2               18                 69
  T3               48                125
  T4               14                 90
[1] 4 2
[1] TRUE
[1] "dimension of 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    22  22  18  19
  15Q LOSS WILD-TYPE 100  85  57  60
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               22                100
  N1               22                 85
  N2               18                 57
  N3               19                 60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  15Q LOSS MUTATED    74   4   6
  15Q LOSS WILD-TYPE 279  20  12
D67V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               74                279
  M1                4                 20
  MX                6                 12
[1] 3 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    33  51
  15Q LOSS WILD-TYPE 118 193
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     33   51
  15Q LOSS WILD-TYPE  118  193
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               33                118
  MALE                 51                193
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  15Q LOSS MUTATED                                      12
  15Q LOSS WILD-TYPE                                    53
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                       26
  15Q LOSS WILD-TYPE                                                    131
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                                  17
  15Q LOSS WILD-TYPE                                                                52
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  15Q LOSS MUTATED                                                 22
  15Q LOSS WILD-TYPE                                               42
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  15Q LOSS MUTATED                                                          1
  15Q LOSS WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  15Q LOSS MUTATED                                                           2
  15Q LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  15Q LOSS MUTATED                                          4
  15Q LOSS WILD-TYPE                                        5
D67V8, multiclass
                                                                   clus
vv                                                                  15Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           12
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          26
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                22
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         4
                                                                   clus
vv                                                                  15Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             53
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           131
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     3  81
  15Q LOSS WILD-TYPE   3 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3   81
  15Q LOSS WILD-TYPE    3  308
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 3                  3
  YES               81                308
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    70   4   3   3
  15Q LOSS WILD-TYPE 248  12  15  22
D67V10, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               70                248
  R1                4                 12
  R2                3                 15
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  15Q LOSS MUTATED      23                         0
  15Q LOSS WILD-TYPE    65                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           0    51
  15Q LOSS WILD-TYPE                                         1   192
D67V12, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                                   23                 65
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   51                192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    60  22
  16P LOSS WILD-TYPE 182 100
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                82                282 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                22                100 
$`16P LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7901 
        6.61         9.21        35.24        15.42        28.01         0.95 
TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       18.71         1.32         0.69        12.95         0.26        16.31 
TCGA-BR-8365 TCGA-BR-8373 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4CQ 
        2.96        14.79         0.49        11.54         0.62        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5803 TCGA-CD-8524 
        0.92         0.72         1.15        13.64         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C 
        0.07         0.07         0.16         6.35         0.13         0.13 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-5724 
        0.10         7.99        29.98        19.07        12.03        12.03 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A6EX TCGA-D7-A6F0 
       11.93        20.55        15.22        12.33        11.31         2.96 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6875 TCGA-HU-8243 
       15.65         7.40         7.79        16.24        72.23         5.92 
TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
       12.59        12.10         0.76        22.75        25.81        11.77 
TCGA-HU-A4GU TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RN 
        6.25        17.69        12.30         9.67        27.42        13.08 
TCGA-IN-A6RR TCGA-KB-A6F5 TCGA-KB-A93H TCGA-RD-A7BS TCGA-RD-A7C1 TCGA-RD-A8N9 
        6.74         5.56        28.90        11.05        16.67        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        5.79        37.74         5.46        46.26         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-A91Z 
        1.87        23.57        64.57        28.70         8.58        44.25 
TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        8.61        40.08        21.11         0.79 

$`16P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 
       24.76        23.93         0.69         0.16        18.54        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 
        0.69        12.76        17.49         0.82        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       20.55         0.72         0.26         1.55         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        6.18        19.50         0.36         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 
        9.21        20.22         1.12        12.79        15.81         2.14 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
       13.45         0.20         7.53        15.81        16.44         0.59 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
       15.68        10.68        12.56         1.15         0.66         3.02 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
       12.82         0.66        19.36        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 
       20.42        11.57         5.13         2.83         3.25        13.15 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
       13.18         0.30         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         0.13         0.13 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.07         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 
       15.95         1.02         8.05        54.08         4.01        14.01 
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       47.05        21.99         9.01        18.97         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.66        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 
        5.95        17.19         4.14        15.98        12.79        10.55 
TCGA-D7-6820 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 
       11.31        24.72        16.80        19.50        17.19         0.23 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV 
        6.97        21.14        20.91        14.27        16.44         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-5647 TCGA-F1-6177 TCGA-F1-6874 
        9.76         4.34         7.13         0.62         6.58        14.47 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27         8.12         0.39        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         1.55 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
        0.23        18.08        26.47         1.51        14.27        14.17 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       11.41        10.62        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       24.20         3.25        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.51        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
        8.88         8.81        21.21         3.45        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RS 
       18.38         5.36         5.19         1.41         6.44         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ 
        5.56         1.81         2.53        60.56         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
        4.31         8.61         4.67       122.30        37.91        40.64 
TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
      115.69       116.38        71.38        57.44         8.94        16.87 
TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        0.92        13.25        13.02        31.10        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PO 
       23.77         7.73        19.07        33.63        16.31         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91D 
       23.41        15.65        19.30        14.33        59.18        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y 
        8.68        49.25        20.81         1.71         7.36         9.73 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 
       55.43         4.54         6.58         5.72        29.98         4.21 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             72.23             122.30 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            11.655             11.635 
[1] "0.1 - 72.2 (11.7)"  "0.1 - 122.3 (11.6)"
[1] "hr=" "1.3"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         0        5        8        9         9        10
  16P LOSS WILD-TYPE       2        8       31       22        27        39
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           0         22         10          8        6
  16P LOSS WILD-TYPE         3         55         45         29       31
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  5                  8
  STAGE IB                  8                 31
  STAGE II                  9                 22
  STAGE IIA                 9                 27
  STAGE IIB                10                 39
  STAGE III                 0                  3
  STAGE IIIA               22                 55
  STAGE IIIB               10                 45
  STAGE IIIC                8                 29
  STAGE IV                  6                 31
[1] 11  2
[1] TRUE
[1] "dimension of 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     5  17  46  20
  16P LOSS WILD-TYPE  16  70 127  84
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                5                 16
  T2               17                 70
  T3               46                127
  T4               20                 84
[1] 4 2
[1] TRUE
[1] "dimension of 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   28 30 15 15
  16P LOSS WILD-TYPE 94 77 60 64
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               28                 94
  N1               30                 77
  N2               15                 60
  N3               15                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16P LOSS MUTATED    84   3   3
  16P LOSS WILD-TYPE 269  21  15
D68V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               84                269
  M1                3                 21
  MX                3                 15
[1] 3 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    35  55
  16P LOSS WILD-TYPE 116 189
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     35   55
  16P LOSS WILD-TYPE  116  189
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               35                116
  MALE                 55                189
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16P LOSS MUTATED                                       9
  16P LOSS WILD-TYPE                                    56
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                       31
  16P LOSS WILD-TYPE                                                    126
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                                  16
  16P LOSS WILD-TYPE                                                                53
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  16P LOSS MUTATED                                                 22
  16P LOSS WILD-TYPE                                               42
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16P LOSS MUTATED                                                          8
  16P LOSS WILD-TYPE                                                       13
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  16P LOSS MUTATED                                                           2
  16P LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16P LOSS MUTATED                                          2
  16P LOSS WILD-TYPE                                        7
D68V8, multiclass
                                                                   clus
vv                                                                  16P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          31
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               16
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                22
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  16P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           126
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 53
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  42
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     2  88
  16P LOSS WILD-TYPE   4 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2   88
  16P LOSS WILD-TYPE    4  301
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 2                  4
  YES               88                301
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    73   4   2   5
  16P LOSS WILD-TYPE 245  12  16  20
D68V10, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               73                245
  R1                4                 12
  R2                2                 16
  RX                5                 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"
D68V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16P LOSS MUTATED      24                         2
  16P LOSS WILD-TYPE    64                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           0    51
  16P LOSS WILD-TYPE                                         1   192
D68V12, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                                   24                 64
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   51                192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    67  26
  16Q LOSS WILD-TYPE 175  96
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                93                271 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                26                 96 
$`16Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 
        6.61        10.13         0.82         9.21        35.24        15.42 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8077 
       28.01        18.54         0.95        18.71         1.32         0.69 
TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8365 TCGA-BR-8373 
        0.49        12.95         0.26        16.31         2.96        14.79 
TCGA-BR-8484 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-A4J1 TCGA-BR-A4PD 
        0.72         0.49        11.54         0.62         0.72        20.65 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
        1.15        13.64        13.15         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH 
        0.07         0.07         0.16         6.35         0.13         0.10 
TCGA-CG-4436 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4475 
        7.99        29.98        47.05        19.07        12.03        22.98 
TCGA-CG-4477 TCGA-CG-5724 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6528 
       30.97        12.03        11.93        20.55        17.19        15.22 
TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-A4YT TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 
       12.79         0.23        14.27        11.31         2.96        15.65 
TCGA-EQ-A4SO TCGA-F1-6875 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8604 TCGA-HU-8610 
       16.24        72.23         5.92        12.59        12.10         0.76 
TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H4 TCGA-HU-A4H5 
       11.77         8.98         6.25         0.26        17.69        12.30 
TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RN TCGA-KB-A6F5 TCGA-KB-A6F7 
        9.67        27.42        18.38        13.08         5.56        60.56 
TCGA-KB-A93H TCGA-RD-A7BS TCGA-RD-A8N9 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
       28.90        11.05        35.61         5.79        37.74         5.46 
TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU 
        7.73        46.26         2.70        17.85         1.87        23.57 
TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 
       64.57        28.70         8.58         9.73        44.25         8.61 
TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-ZQ-A9CR 
        4.54        40.08         0.79 

$`16Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       13.12        13.68         7.00        39.12         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 TCGA-BR-7707 
       30.90        31.20        32.94        12.82        24.76        23.93 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 
        0.69         0.16        12.43         0.69        12.76        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 
        0.82        12.26        20.55         0.72         0.26         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.48         7.40         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
       22.19         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        0.36        19.17         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39         9.21        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 
        2.14        13.45         0.20         7.53        15.81        16.44 
TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
        0.59        15.68        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        3.02        22.26         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 
        0.79        14.17         0.53        12.82         0.66        19.36 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       13.51         0.46        20.42        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 
        3.25        13.18         0.07         0.10         0.13         0.10 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A489 
        0.10         0.13         0.13         0.10         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 
        0.13         0.07         0.10         0.10        20.02         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 
       27.02        15.95         1.02         8.05        54.08         4.01 
TCGA-CG-4441 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 
       14.01        21.99         9.01        18.97         7.07        12.00 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        15.02        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       55.04        21.07         7.99        12.36        12.66        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6527 
       18.84        18.54        18.61        17.85         5.95         4.14 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU 
       19.50        17.19         6.97        21.14        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-5647 
       11.44         9.76         4.34         7.40         7.13         0.62 
TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
        7.79         6.58        14.47        21.27         8.12         0.39 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 
       19.53         3.02        22.29        17.06        59.54         5.03 
TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 
       13.58         0.56         1.55         0.23        18.08        26.47 
TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G2 
        1.51        14.27        14.17        11.41        10.62        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX 
       25.81        21.37        29.98         0.10         6.51        10.19 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 
        2.10        12.95        19.36         8.88         8.81        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO 
        3.45        18.81         3.39         5.36         5.19         1.41 
TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 
        6.44         6.74         6.87         5.56         1.81         2.53 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
        3.72        19.73         4.31         8.61         4.67        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 
      122.30        37.91        40.64       115.69       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       57.44         8.94        16.87         0.92        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       31.10        21.73        22.36        23.77        19.07        33.63 
TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PY 
       16.31         9.27        23.41        15.65        19.30        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       59.18        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J 
        7.36        55.43         6.58         5.72        29.98        21.11 
TCGA-ZA-A8F6 
        4.21 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.07 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             72.23             122.30 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             11.54              11.70 
[1] "0.1 - 72.2 (11.5)"  "0.1 - 122.3 (11.7)"
[1] "hr=" "1.2"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         0        5        9       12        10        10
  16Q LOSS WILD-TYPE       2        8       30       19        26        39
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           0         27         11          9        6
  16Q LOSS WILD-TYPE         3         50         44         28       31
D69V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  5                  8
  STAGE IB                  9                 30
  STAGE II                 12                 19
  STAGE IIA                10                 26
  STAGE IIB                10                 39
  STAGE III                 0                  3
  STAGE IIIA               27                 50
  STAGE IIIB               11                 44
  STAGE IIIC                9                 28
  STAGE IV                  6                 31
[1] 11  2
[1] TRUE
[1] "dimension of 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     7  20  51  22
  16Q LOSS WILD-TYPE  14  67 122  82
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                7                 14
  T2               20                 67
  T3               51                122
  T4               22                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  16Q LOSS MUTATED   32 30 18 19
  16Q LOSS WILD-TYPE 90 77 57 60
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               32                 90
  N1               30                 77
  N2               18                 57
  N3               19                 60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16Q LOSS MUTATED    96   3   2
  16Q LOSS WILD-TYPE 257  21  16
D69V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               96                257
  M1                3                 21
  MX                2                 16
[1] 3 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    42  59
  16Q LOSS WILD-TYPE 109 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     42   59
  16Q LOSS WILD-TYPE  109  185
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               42                109
  MALE                 59                185
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  16Q LOSS MUTATED                                      13
  16Q LOSS WILD-TYPE                                    52
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                       32
  16Q LOSS WILD-TYPE                                                    125
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                                  17
  16Q LOSS WILD-TYPE                                                                52
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  16Q LOSS MUTATED                                                 24
  16Q LOSS WILD-TYPE                                               40
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  16Q LOSS MUTATED                                                          9
  16Q LOSS WILD-TYPE                                                       12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  16Q LOSS MUTATED                                                           3
  16Q LOSS WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  16Q LOSS MUTATED                                          2
  16Q LOSS WILD-TYPE                                        7
D69V8, multiclass
                                                                   clus
vv                                                                  16Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           13
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          32
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  16Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             52
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           125
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3  98
  16Q LOSS WILD-TYPE   3 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   98
  16Q LOSS WILD-TYPE    3  291
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 3                  3
  YES               98                291
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    84   4   4   4
  16Q LOSS WILD-TYPE 234  12  14  21
D69V10, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               84                234
  R1                4                 12
  R2                4                 14
  RX                4                 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"
D69V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  16Q LOSS MUTATED      26                         1
  16Q LOSS WILD-TYPE    62                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           0    57
  16Q LOSS WILD-TYPE                                         1   186
D69V12, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                                   26                 62
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   57                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"

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    92  44
  17P LOSS WILD-TYPE 150  78
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               136                228 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                44                 78 
$`17P LOSS MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6565 
       11.70         6.61         6.18        10.13         7.00         0.62 
TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7723 TCGA-BR-7959 
        1.25         9.21        35.24        15.42        18.54        18.71 
TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8296 
        0.69         0.49        12.95         0.26        16.31         1.48 
TCGA-BR-8362 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8678 
        0.36        14.04        14.79         5.39         0.72        11.54 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       16.44         0.59        10.68         1.15         0.66        22.26 
TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
        0.92         0.72        13.51        20.65        20.42         1.15 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 
        3.25        13.15         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.13         0.13         6.35         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 
        0.13         0.10        20.02         3.02        27.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        8.05        54.08         4.01        29.98        47.05        19.07 
TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5725 TCGA-CG-5727 TCGA-CG-5730 
        7.07        30.97         1.02        15.02        79.07         4.01 
TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6525 
       55.04        11.93        20.55        18.84        18.54         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-8576 
       17.19         4.14        15.22        15.98        11.31         6.97 
TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-8122 TCGA-F1-A72C 
       16.44        11.31        15.65         7.40         7.79         8.12 
TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8245 
        3.02        17.06        13.58         0.23         1.51        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU 
       14.17        12.10        22.75        11.77         8.98         6.25 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
        2.10        12.95        12.30        21.21        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NU TCGA-IP-7968 
       18.38         5.19         1.41         6.87         1.81         2.53 
TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 
        5.56        28.90         4.31         8.61        16.67       115.69 
TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        8.94         5.79         0.92         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM 
       31.10         7.73        46.26         2.70        17.85         1.87 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91Q TCGA-VQ-A91X 
       23.57        64.57        14.33        59.18        20.81         8.58 
TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       40.08        29.98        21.11         0.79 

$`17P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6457 
        9.57         6.61        34.68        15.95        13.12        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       39.12         0.82        32.78        13.84        13.22        16.14 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       24.76        23.93        28.01         0.69         0.16        12.43 
TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 
        0.95         0.69        12.76        17.49         0.82         1.32 
TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8295 TCGA-BR-8297 
       12.26        20.55         0.72         0.26         1.55         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
        6.18        19.50         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 
       13.74         4.31         3.32         0.36        19.17         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        0.26        15.85         3.72         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 
        0.49        15.81        15.68         0.62        12.56         3.02 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-BR-A4QL 
       12.82         0.66        19.36         0.46        13.64        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 
        5.13         2.83        13.18         0.30         0.07         0.07 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A4MG 
        0.16         0.10         0.10         0.10         0.13         0.07 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4455 
        0.10         0.10        15.95         1.02        14.01        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
       21.99         9.01        18.97        12.00        22.98         6.97 
TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
        1.02         0.99         6.02         0.99       105.07        12.03 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       28.96        65.10        21.07         7.99        12.36        12.66 
TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 
       19.13        18.61        17.85        12.79        10.55        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 
       24.72        16.80        19.50        17.19         0.23        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       20.91        14.27         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 
       13.71        11.24        11.44         9.76         2.96         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62        16.24         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
       21.27         0.39        19.53        22.29        59.54         5.03 
TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8243 TCGA-HU-8244 
        0.56         1.55        18.08        26.47         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       11.41        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN 
       11.84        24.20         3.25        25.81        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 
        0.10         6.51        10.19         0.26        19.36        17.69 
TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RJ 
        9.67         8.88         8.81        27.42         3.45         5.36 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-MX-A5UG 
       13.08         6.44         6.74         5.56        60.56         3.72 
TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 
       19.73        11.05         4.67       122.30        37.91        40.64 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DT 
      116.38        71.38        57.44        35.61        16.87        37.74 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       21.73        22.36        23.77        19.07        33.63        16.31 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91A TCGA-VQ-A91D 
        9.27        23.41        15.65        19.30        28.70        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A91Z 
        8.68        49.25         1.71         7.36         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-ZA-A8F6 
        8.61        55.43         4.54         6.58         5.72         4.21 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.07               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            115.69             122.30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             9.095             12.280 
[1] "0.1 - 115.7 (9.1)"  "0.1 - 122.3 (12.3)"
[1] "hr=" "1"  
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         0        5       15       14        13        17
  17P LOSS WILD-TYPE       2        8       24       17        23        32
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           0         29         22         10       15
  17P LOSS WILD-TYPE         3         48         33         27       22
D70V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  5                  8
  STAGE IB                 15                 24
  STAGE II                 14                 17
  STAGE IIA                13                 23
  STAGE IIB                17                 32
  STAGE III                 0                  3
  STAGE IIIA               29                 48
  STAGE IIIB               22                 33
  STAGE IIIC               10                 27
  STAGE IV                 15                 22
[1] 11  2
[1] TRUE
[1] "dimension of 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     6  36  67  32
  17P LOSS WILD-TYPE  15  51 106  72
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                6                 15
  T2               36                 51
  T3               67                106
  T4               32                 72
[1] 4 2
[1] TRUE
[1] "dimension of 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   46 37 30 28
  17P LOSS WILD-TYPE 76 70 45 51
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               46                 76
  N1               37                 70
  N2               30                 45
  N3               28                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  17P LOSS MUTATED   127   8   8
  17P LOSS WILD-TYPE 226  16  10
D70V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0              127                226
  M1                8                 16
  MX                8                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    48  95
  17P LOSS WILD-TYPE 103 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     48   95
  17P LOSS WILD-TYPE  103  149
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               48                103
  MALE                 95                149
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17P LOSS MUTATED                                      14
  17P LOSS WILD-TYPE                                    51
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                       50
  17P LOSS WILD-TYPE                                                    107
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                                  32
  17P LOSS WILD-TYPE                                                                37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  17P LOSS MUTATED                                                 28
  17P LOSS WILD-TYPE                                               36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17P LOSS MUTATED                                                         10
  17P LOSS WILD-TYPE                                                       11
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  17P LOSS MUTATED                                                           4
  17P LOSS WILD-TYPE                                                         4
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17P LOSS MUTATED                                          5
  17P LOSS WILD-TYPE                                        4
D70V8, multiclass
                                                                   clus
vv                                                                  17P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           14
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          50
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        10
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         5
                                                                   clus
vv                                                                  17P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             51
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           107
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          11
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           4
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4 139
  17P LOSS WILD-TYPE   2 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  139
  17P LOSS WILD-TYPE    2  250
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 4                  2
  YES              139                250
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   117   7   6   5
  17P LOSS WILD-TYPE 201   9  12  20
D70V10, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              117                201
  R1                7                  9
  R2                6                 12
  RX                5                 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"
D70V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17P LOSS MUTATED      34                         2
  17P LOSS WILD-TYPE    54                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           1    81
  17P LOSS WILD-TYPE                                         0   162
D70V12, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                                   34                 54
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   81                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"

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    43  22
  17Q LOSS WILD-TYPE 199 100
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                65                299 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                100 
$`17Q LOSS MUTATED`
TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-7959 TCGA-BR-8077 
        7.00         0.62        35.24        18.54        18.71         0.69 
TCGA-BR-8291 TCGA-BR-8373 TCGA-BR-8485 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A452 
       16.31        14.79         9.21         0.59        10.68         0.66 
TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J8 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 
       22.26         0.72        13.51        20.65         1.15         3.25 
TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8533 TCGA-CD-A489 TCGA-CD-A48C TCGA-CD-A4MH 
        0.07         0.10         0.13         0.13         0.13         0.10 
TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 
       20.02         3.02        54.08         4.01        47.05        19.07 
TCGA-CG-4477 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 
       30.97        11.93        20.55        17.19         4.14        15.22 
TCGA-D7-6820 TCGA-D7-8576 TCGA-D7-A6EX TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-FP-A8CX 
       11.31         6.97        11.31        15.65         7.79         0.23 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-IN-8663 TCGA-KB-A6F5 
       12.59        14.17        22.75         8.98         3.39         5.56 
TCGA-KB-A93H TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N6 
       28.90         4.31         8.61        16.67       115.69         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX 
        5.79         5.46        46.26        17.85         1.87        64.57 
TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        8.58         9.73        29.98        21.11         0.79 

$`17Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 
       18.35        30.90         6.18         9.57         6.61        34.68 
TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       15.95        13.12        10.13        13.68        39.12         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8059 
       12.43         0.95         0.69        12.76        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        1.32        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 
       12.95         0.26         1.55         1.48         7.40         6.18 
TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 
       19.50         0.36         0.26        22.19         2.96         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 
       13.74         4.31        14.04         3.32         0.36        19.17 
TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
        0.69         0.26        15.85         3.72         5.39         0.72 
TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 
       20.22         1.12        12.79        15.81         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 
        0.20         7.53         0.49        11.54        15.81        16.44 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4CS 
       15.68         0.62        12.56         1.15         3.02         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI 
       12.82         0.66        19.36         0.46        20.42        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       11.57         5.13         2.83        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
        0.07         0.07         0.07         0.07         0.13         0.16 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
        0.10         0.10         0.13         0.10         6.35         0.13 
TCGA-CD-A48A TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4304 TCGA-CG-4305 
        0.13         0.07         0.10         0.10        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
        1.02         7.99         8.05        14.01        29.98        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         9.01        18.97         7.07        12.00        22.98 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
      105.07        12.03        15.02        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        55.04        21.07         7.99        12.36        12.66 
TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 
       19.13        18.84        18.54        18.61        17.85         5.95 
TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.98        12.79        10.55        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       19.50        17.19         0.23        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74A 
       11.24        11.44         9.76         2.96         4.34         7.40 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        7.13         0.62        16.24         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27         8.12         0.39        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         1.55 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 
       18.08        26.47         1.51         5.92        14.27        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ 
       11.84        24.20         3.25        25.81        11.77        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY 
       29.98         0.10         6.51         6.25        10.19         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 
        2.10        12.95        19.36        17.69        12.30         9.67 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        8.88         8.81        27.42        21.21         3.45        18.81 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RP 
       18.38         5.36         5.19        13.08         1.41         6.44 
TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F7 
        6.74         6.87         5.56         1.81         2.53        60.56 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        3.72        19.73        11.05         4.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N9 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44        35.61        16.87 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 
        0.92        37.74        13.25        13.02        31.10        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PD 
       22.36        23.77         7.73        19.07        33.63        16.31 
TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU 
        2.70         9.27        23.41        15.65        19.30        23.57 
TCGA-VQ-A8PY TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       14.33        59.18        28.70        11.70         8.68        49.25 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
       20.81         1.71         7.36        44.25         8.61        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-ZA-A8F6 
        4.54         6.58         5.72        40.08         4.21 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.07               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            115.69             122.30 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              9.73              11.84 
[1] "0.1 - 115.7 (9.7)"  "0.1 - 122.3 (11.8)"
[1] "hr=" "1"  
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         0        1        5        6         5        10
  17Q LOSS WILD-TYPE       2       12       34       25        31        39
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           0         16         14          4        5
  17Q LOSS WILD-TYPE         3         61         41         33       32
D71V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 12
  STAGE IB                  5                 34
  STAGE II                  6                 25
  STAGE IIA                 5                 31
  STAGE IIB                10                 39
  STAGE III                 0                  3
  STAGE IIIA               16                 61
  STAGE IIIB               14                 41
  STAGE IIIC                4                 33
  STAGE IV                  5                 32
[1] 11  2
[1] TRUE
[1] "dimension of 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     1  15  32  19
  17Q LOSS WILD-TYPE  20  72 141  85
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                1                 20
  T2               15                 72
  T3               32                141
  T4               19                 85
[1] 4 2
[1] TRUE
[1] "dimension of 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    16  21  18  12
  17Q LOSS WILD-TYPE 106  86  57  67
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               16                106
  N1               21                 86
  N2               18                 57
  N3               12                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  17Q LOSS MUTATED    63   2   4
  17Q LOSS WILD-TYPE 290  22  14
D71V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0               63                290
  M1                2                 22
  MX                4                 14
[1] 3 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    27  42
  17Q LOSS WILD-TYPE 124 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     27   42
  17Q LOSS WILD-TYPE  124  202
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               27                124
  MALE                 42                202
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  17Q LOSS MUTATED                                       7
  17Q LOSS WILD-TYPE                                    58
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                       22
  17Q LOSS WILD-TYPE                                                    135
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                                  17
  17Q LOSS WILD-TYPE                                                                52
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  17Q LOSS MUTATED                                                 14
  17Q LOSS WILD-TYPE                                               50
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  17Q LOSS MUTATED                                                          4
  17Q LOSS WILD-TYPE                                                       17
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  17Q LOSS MUTATED                                                           2
  17Q LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  17Q LOSS MUTATED                                          3
  17Q LOSS WILD-TYPE                                        6
D71V8, multiclass
                                                                   clus
vv                                                                  17Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            7
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          22
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                14
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         4
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  17Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             58
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           135
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  50
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     1  68
  17Q LOSS WILD-TYPE   5 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   68
  17Q LOSS WILD-TYPE    5  321
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                  5
  YES               68                321
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    55   2   4   3
  17Q LOSS WILD-TYPE 263  14  14  22
D71V10, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               55                263
  R1                2                 14
  R2                4                 14
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  17Q LOSS MUTATED      15                         1
  17Q LOSS WILD-TYPE    73                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           1    42
  17Q LOSS WILD-TYPE                                         0   201
D71V12, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                                   15                 73
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   42                201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    71  24
  18P LOSS WILD-TYPE 171  98
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                95                269 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                24                 98 
$`18P LOSS MUTATED`
TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 
        9.57        10.13        13.68         0.82         1.25        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7957 TCGA-BR-8289 TCGA-BR-8291 
       15.42        28.01        18.54         0.69         0.26        16.31 
TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8677 
       22.19         0.95        14.04         0.72        15.81         0.49 
TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 
       11.54         0.59        15.68        10.68         1.15         0.66 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8524 
       22.26         0.92        12.89        13.18         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.10         0.13         0.10         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
        0.13         0.13         0.13         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5719 
        4.01        47.05        19.07         7.07        30.97         1.02 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6815 TCGA-D7-8573 
       19.13        20.55        18.54         5.95        15.98        19.50 
TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ 
        0.23        21.14        16.44        15.16        11.24         9.76 
TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
        0.62        72.23         8.12        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8238 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8604 
       17.06         0.23         1.51        12.59        14.17        12.10 
TCGA-HU-8608 TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 
       10.62        12.30        11.77         8.98         6.25         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-A6RL TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
       12.95         9.67         5.19         1.81         5.56        28.90 
TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ 
       16.67       115.69         5.79        37.74         5.46        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8PD TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-AA6B 
       31.10        16.31        44.25         4.54        29.98 

$`18P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         6.18         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 
       13.12         7.00        39.12         0.62        32.78        13.84 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 
       13.22        16.14         8.98        21.11        30.90        31.20 
TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 
       32.94        12.82         9.21        24.76        23.93         0.69 
TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
        0.16        12.43         0.95        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
        0.82         1.32         0.69        12.26         0.49        20.55 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
        0.72         0.26        12.95         1.55         1.48         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 
        6.18        19.50         0.36         0.26         2.96        13.74 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 
        4.31         3.32         0.36        19.17        14.79         0.69 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 
        0.26        15.85         3.72         5.39         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
        1.12        12.79         2.14        13.45         0.20         7.53 
TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       15.81        16.44         0.62        12.56         3.02        13.41 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 
       13.51         0.79         0.72        14.17         0.53        12.82 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE 
        0.66        19.36        13.51         0.46        20.65        20.42 
TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 
        1.15        13.64        11.57         5.13         2.83         3.25 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 
       13.15         0.30         0.07         0.16         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI 
        0.10         6.35         0.13         0.07         0.10         0.10 
TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10        20.02         3.02        27.02        15.95         1.02 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 
       14.01        29.98        12.03        21.99         9.01        18.97 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 
       12.00        22.98         6.97         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       12.66        11.93        18.84        18.61        17.85        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
        4.14        15.22        12.79        10.55        11.31        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT 
       24.72        16.80        17.19         6.97        20.91        14.27 
TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY 
        5.92        13.78        14.76        13.71        11.31        11.44 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 
        2.96        15.65         4.34         7.40         7.13         7.79 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 
       16.24         6.58        14.47        21.27         0.39        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 
        5.03        13.58         0.56         1.55        18.08        26.47 
TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
        5.92        14.27        11.41         0.76        24.30         5.59 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 
       29.98         0.10         6.51        10.19         0.26        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 
       17.69        12.30         8.88         8.81        27.42        21.21 
TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN 
        3.45        18.81         3.39        18.38         5.36        13.08 
TCGA-IN-A6RO TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IP-7968 
        1.41         6.44         6.74         6.87         5.56         2.53 
TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT 
       60.56         3.72        19.73         4.31        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
        4.67       122.30        37.91        40.64       116.38        71.38 
TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8DV 
       57.44         8.94        35.61        16.87         0.92        13.25 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP 
       46.26         2.70        17.85         1.87         9.27        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       15.65        19.30        23.57        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       28.70        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
        7.36         8.58         9.73         8.61        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        40.08        21.11         4.21         0.79 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.07               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            115.69             122.30 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             10.62              11.93 
[1] "0.1 - 115.7 (10.6)" "0.1 - 122.3 (11.9)"
[1] "hr=" "1.3"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         0        3        5       10        12        11
  18P LOSS WILD-TYPE       2       10       34       21        24        38
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED           0         24         16          8        9
  18P LOSS WILD-TYPE         3         53         39         29       28
D72V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 10
  STAGE IB                  5                 34
  STAGE II                 10                 21
  STAGE IIA                12                 24
  STAGE IIB                11                 38
  STAGE III                 0                  3
  STAGE IIIA               24                 53
  STAGE IIIB               16                 39
  STAGE IIIC                8                 29
  STAGE IV                  9                 28
[1] 11  2
[1] TRUE
[1] "dimension of 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     2  20  55  22
  18P LOSS WILD-TYPE  19  67 118  82
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                2                 19
  T2               20                 67
  T3               55                118
  T4               22                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18P LOSS MUTATED   29 25 22 23
  18P LOSS WILD-TYPE 93 82 53 56
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               29                 93
  N1               25                 82
  N2               22                 53
  N3               23                 56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  18P LOSS MUTATED    90   7   4
  18P LOSS WILD-TYPE 263  17  14
D72V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               90                263
  M1                7                 17
  MX                4                 14
[1] 3 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    31  70
  18P LOSS WILD-TYPE 120 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     31   70
  18P LOSS WILD-TYPE  120  174
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               31                120
  MALE                 70                174
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18P LOSS MUTATED                                      18
  18P LOSS WILD-TYPE                                    47
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                       38
  18P LOSS WILD-TYPE                                                    119
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                                  17
  18P LOSS WILD-TYPE                                                                52
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  18P LOSS MUTATED                                                 19
  18P LOSS WILD-TYPE                                               45
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18P LOSS MUTATED                                                          5
  18P LOSS WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  18P LOSS MUTATED                                                           2
  18P LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18P LOSS MUTATED                                          2
  18P LOSS WILD-TYPE                                        7
D72V8, multiclass
                                                                   clus
vv                                                                  18P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           18
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          38
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               17
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  18P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             47
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           119
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 52
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  45
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     0 101
  18P LOSS WILD-TYPE   6 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0  101
  18P LOSS WILD-TYPE    6  288
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 0                  6
  YES              101                288
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    83   4   4   5
  18P LOSS WILD-TYPE 235  12  14  20
D72V10, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               83                235
  R1                4                 12
  R2                4                 14
  RX                5                 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"
D72V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED      33                         2
  18P LOSS WILD-TYPE    55                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           0    55
  18P LOSS WILD-TYPE                                         1   188
D72V12, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                                   33                 55
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   55                188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    89  36
  18Q LOSS WILD-TYPE 153  86
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               125                239 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                36                 86 
$`18Q LOSS MUTATED`
TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 
       11.70         6.61         6.18         9.57        10.13        13.68 
TCGA-BR-6564 TCGA-BR-6709 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
        0.82         1.25        35.24        15.42        28.01        18.54 
TCGA-BR-7957 TCGA-BR-8060 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8369 
        0.69         1.32        16.31        22.19         0.95        14.04 
TCGA-BR-8370 TCGA-BR-8486 TCGA-BR-8589 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 
        3.32        20.22        15.81         0.49        11.54         0.59 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A4CQ 
       15.68         0.62        10.68         1.15         0.66        22.26 
TCGA-BR-A4IY TCGA-BR-A4J6 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 
       12.89         0.66        13.18         0.30         0.07         0.07 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8532 
        0.07         0.07         0.07         0.10         0.13         0.10 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4301 
        0.13         6.35         0.13         0.13         0.10         3.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4449 
        7.99         8.05        54.08         4.01        47.05        19.07 
TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 
       18.97         7.07        22.98        30.97         1.02        12.03 
TCGA-CG-5730 TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6525 
        4.01        12.36        19.13        20.55        18.54         5.95 
TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 
       17.19         4.14        15.98        19.50         0.23         6.97 
TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F0 
       21.14        16.44        15.16        11.24         9.76         2.96 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C 
       15.65         7.40         0.62         7.79        72.23         8.12 
TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-A8CX TCGA-HU-8245 
       19.53         3.02        22.29        17.06         0.23        12.59 
TCGA-HU-8249 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-HU-A4GP 
       14.17        12.10        10.62        12.30        11.77         8.98 
TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-IN-A6RL TCGA-IN-A6RO 
        6.25         2.10        12.95         9.67         5.19         1.41 
TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        6.74         5.56         1.81         5.56        60.56        28.90 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8DU 
       16.67        37.91       115.69         5.79        37.74         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PD TCGA-VQ-A8PK 
       13.25        13.02        31.10         7.73        16.31        17.85 
TCGA-VQ-A8PU TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A925 TCGA-VQ-AA6B 
       23.57         8.58        44.25         4.54        29.98 

$`18Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 TCGA-BR-4201 
        5.62         6.97         4.64         7.43        18.35        30.90 
TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6563 
        6.61        34.68        15.95        13.12         7.00        39.12 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6710 
        0.62        32.78        13.84        13.22        16.14         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       24.76        23.93         0.69         0.16        12.43         0.95 
TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8077 TCGA-BR-8078 
       12.76        18.71        17.49         0.82         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49        20.55         0.72         0.26        12.95         0.26 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 
        1.55         1.48         7.40         6.18        19.50         0.36 
TCGA-BR-8363 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 
        0.26         2.96        13.74         4.31         0.36        19.17 
TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 
       14.79         0.69         0.26        15.85         3.72         5.39 
TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 
        0.72         9.21         1.12        12.79         2.14        13.45 
TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 
        0.20         7.53        15.81        16.44        12.56         3.02 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 
        0.92        13.41        13.51         0.79         0.72        14.17 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD 
        0.53        12.82        19.36        13.51         0.46        20.65 
TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
       20.42         1.15        13.64        11.57         5.13         2.83 
TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8535 TCGA-CD-8536 
        3.25        13.15         0.16         0.10         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.13         0.07         0.10         0.10        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
       27.02        15.95         1.02        14.01        29.98        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5720 
       21.99         9.01        12.00         6.97         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        6.02         0.99       105.07        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-5579 
       65.10        55.04        21.07         7.99        12.66        11.93 
TCGA-D7-6520 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6818 
       18.84        18.61        17.85        15.22        12.79        10.55 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8579 
       11.31        12.33        24.72        16.80        17.19        20.91 
TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EX 
       14.27         5.92        13.78        14.76        13.71        11.31 
TCGA-D7-A6EY TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
       11.44         4.34         7.13        16.24         6.58        14.47 
TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 
       21.27         0.39        59.54         5.03        13.58         0.56 
TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        1.55        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8602 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       11.41         0.76        24.30         5.59        11.84        24.20 
TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ 
        3.25        22.75        25.81        21.37        29.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
        6.51        10.19         0.26        19.36        17.69        12.30 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
        8.88         8.81        27.42        21.21         3.45        18.81 
TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RS 
        3.39        18.38         5.36        13.08         6.44         6.87 
TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT 
        2.53         3.72        19.73         4.31        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
        4.67       122.30        40.64       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8DL TCGA-VQ-A8E3 TCGA-VQ-A8P2 
        8.94        35.61        16.87         0.92        21.73        22.36 
TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PJ TCGA-VQ-A8PM 
       23.77        19.07        33.63        46.26         2.70         1.87 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        9.27        23.41        15.65        19.30        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       59.18        28.70        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 
        1.71         7.36         9.73         8.61        55.43         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
        5.72        40.08        21.11         4.21         0.79 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            115.69             122.30 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              9.76              12.26 
[1] "0.1 - 115.7 (9.8)"  "0.1 - 122.3 (12.3)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         0        5       12       12        15        14
  18Q LOSS WILD-TYPE       2        8       27       19        21        35
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED           0         30         22          8       11
  18Q LOSS WILD-TYPE         3         47         33         29       26
D73V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  5                  8
  STAGE IB                 12                 27
  STAGE II                 12                 19
  STAGE IIA                15                 21
  STAGE IIB                14                 35
  STAGE III                 0                  3
  STAGE IIIA               30                 47
  STAGE IIIB               22                 33
  STAGE IIIC                8                 29
  STAGE IV                 11                 26
[1] 11  2
[1] TRUE
[1] "dimension of 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    5 30 74 22
  18Q LOSS WILD-TYPE 16 57 99 82
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                5                 16
  T2               30                 57
  T3               74                 99
  T4               22                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18Q LOSS MUTATED   41 36 27 26
  18Q LOSS WILD-TYPE 81 71 48 53
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               41                 81
  N1               36                 71
  N2               27                 48
  N3               26                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  18Q LOSS MUTATED   118   9   6
  18Q LOSS WILD-TYPE 235  15  12
D73V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0              118                235
  M1                9                 15
  MX                6                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    50  83
  18Q LOSS WILD-TYPE 101 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     50   83
  18Q LOSS WILD-TYPE  101  161
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               50                101
  MALE                 83                161
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  18Q LOSS MUTATED                                      20
  18Q LOSS WILD-TYPE                                    45
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                       51
  18Q LOSS WILD-TYPE                                                    106
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                                  27
  18Q LOSS WILD-TYPE                                                                42
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  18Q LOSS MUTATED                                                 24
  18Q LOSS WILD-TYPE                                               40
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  18Q LOSS MUTATED                                                          5
  18Q LOSS WILD-TYPE                                                       16
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  18Q LOSS MUTATED                                                           3
  18Q LOSS WILD-TYPE                                                         5
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  18Q LOSS MUTATED                                          2
  18Q LOSS WILD-TYPE                                        7
D73V8, multiclass
                                                                   clus
vv                                                                  18Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           20
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          51
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               27
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                24
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         5
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        3
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  18Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             45
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           106
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 42
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  40
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          16
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          5
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     1 132
  18Q LOSS WILD-TYPE   5 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1  132
  18Q LOSS WILD-TYPE    5  257
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 1                  5
  YES              132                257
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   104   6   7   8
  18Q LOSS WILD-TYPE 214  10  11  17
D73V10, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              104                214
  R1                6                 10
  R2                7                 11
  RX                8                 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"
D73V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  18Q LOSS MUTATED      36                         2
  18Q LOSS WILD-TYPE    52                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           0    77
  18Q LOSS WILD-TYPE                                         1   166
D73V12, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                                   36                 52
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   77                166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    56  38
  19P LOSS WILD-TYPE 186  84
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                94                270 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                38                 84 
$`19P LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 
        6.61         0.62        35.24        28.01        18.54         0.95 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 
        1.32         0.69         0.26         1.55        14.04        14.79 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
        9.21        11.54        10.68        22.26         0.92         0.72 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8524 TCGA-CD-8525 
       20.65         1.15         3.25        13.15         0.07         0.07 
TCGA-CD-8527 TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 
        0.07         6.35         0.13         0.13         0.10        20.02 
TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4466 TCGA-CG-5724 
        7.99        54.08         4.01        29.98        18.97        12.03 
TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6817 
       15.02        55.04        18.84         5.95         4.14        12.79 
TCGA-D7-6820 TCGA-D7-8573 TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 
       11.31        19.50        11.31         2.96        15.65         0.62 
TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7916 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-8243 
        7.79        72.23         3.02        17.06         0.56         5.92 
TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H4 
       12.59        11.77         8.98         6.25         2.10        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RO 
       12.30         9.67        27.42         3.39        18.38         1.41 
TCGA-IN-A6RS TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        6.87         5.56         1.81         5.56        60.56        28.90 
TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.61         4.67        37.91         8.94         0.92        37.74 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PK 
        5.46        13.25        13.02        31.10         7.73        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z 
        1.87        23.57         1.71         8.58         9.73        44.25 
TCGA-VQ-A922 TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        8.61        40.08        21.11         0.79 

$`19P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 
       24.76        23.93        15.42         0.69         0.16        12.43 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8078 
        0.69        12.76        18.71        17.49         0.82        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 
        0.49        20.55         0.72         0.26        12.95        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.48         7.40         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19         2.96         0.95        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 
        0.36        19.17         0.69         0.26        15.85         3.72 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 
        5.39         0.72        20.22         1.12        12.79        15.81 
TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 
        2.14        13.45         0.20         7.53         0.49        15.81 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T TCGA-BR-A44U 
       16.44         0.59        15.68         0.62        12.56         1.15 
TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        0.66         3.02        13.41        13.51        12.89         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42        13.64        11.57         5.13         2.83 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8526 TCGA-CD-8528 TCGA-CD-8529 
       13.18         0.30         0.07         0.07         0.10         0.13 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-8536 
        0.16         0.10         0.10         0.13         0.13         0.10 
TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 
        0.13         0.13         0.07         0.10         0.10         3.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4444 
       27.02        15.95         1.02         8.05        14.01        47.05 
TCGA-CG-4449 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 
       19.07        12.03        21.99         9.01         7.07        12.00 
TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 
       22.98        30.97         6.97         1.02         1.02         0.99 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 
        6.02         0.99       105.07        28.96        79.07        65.10 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
        4.01        21.07         7.99        12.36        12.66        11.93 
TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6526 
       19.13        20.55        18.54        18.61        17.85        17.19 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       15.22        15.98        10.55        12.33        24.72        16.80 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT 
       17.19         0.23         6.97        21.14        20.91        14.27 
TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET 
       16.44         5.92        15.16        13.78        14.76        13.71 
TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-D7-A74B 
       11.24        11.44         9.76         4.34         7.40         7.13 
TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 
       16.24         6.58        14.47        21.27         8.12         0.39 
TCGA-FP-7829 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF 
       19.53        22.29        59.54         5.03        13.58         1.55 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 
        0.23        18.08        26.47         1.51        14.27        14.17 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       11.41        12.10        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY 
       21.37        29.98         0.10         6.51        10.19         0.26 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.95        19.36         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR 
       18.81         5.36         5.19        13.08         6.44         6.74 
TCGA-IP-7968 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7C1 
        2.53         3.72        19.73         4.31        11.05        16.67 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
      122.30        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       35.61        16.87         5.79        21.73        22.36        23.77 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       19.07        33.63        46.26        16.31         2.70         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        19.30        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91W 
       28.70        11.70         8.68        49.25        20.81         7.36 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-ZA-A8F6 
       55.43         4.54         6.58         5.72        29.98         4.21 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.07               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             72.23             122.30 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              8.96              12.28 
[1] "0.1 - 72.2 (9.0)"   "0.1 - 122.3 (12.3)"
[1] "hr=" "1.4"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         0        5       11        6        11        12
  19P LOSS WILD-TYPE       2        8       28       25        25        37
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           0         21         12         10       10
  19P LOSS WILD-TYPE         3         56         43         27       27
D74V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  5                  8
  STAGE IB                 11                 28
  STAGE II                  6                 25
  STAGE IIA                11                 25
  STAGE IIB                12                 37
  STAGE III                 0                  3
  STAGE IIIA               21                 56
  STAGE IIIB               12                 43
  STAGE IIIC               10                 27
  STAGE IV                 10                 27
[1] 11  2
[1] TRUE
[1] "dimension of 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     6  23  44  25
  19P LOSS WILD-TYPE  15  64 129  79
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                6                 15
  T2               23                 64
  T3               44                129
  T4               25                 79
[1] 4 2
[1] TRUE
[1] "dimension of 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   31 24 19 24
  19P LOSS WILD-TYPE 91 83 56 55
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               31                 91
  N1               24                 83
  N2               19                 56
  N3               24                 55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  19P LOSS MUTATED    90   5   5
  19P LOSS WILD-TYPE 263  19  13
D74V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               90                263
  M1                5                 19
  MX                5                 13
[1] 3 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    36  64
  19P LOSS WILD-TYPE 115 180
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     36   64
  19P LOSS WILD-TYPE  115  180
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               36                115
  MALE                 64                180
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19P LOSS MUTATED                                       9
  19P LOSS WILD-TYPE                                    56
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                       36
  19P LOSS WILD-TYPE                                                    121
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                                  28
  19P LOSS WILD-TYPE                                                                41
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  19P LOSS MUTATED                                                 20
  19P LOSS WILD-TYPE                                               44
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19P LOSS MUTATED                                                          1
  19P LOSS WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  19P LOSS MUTATED                                                           4
  19P LOSS WILD-TYPE                                                         4
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19P LOSS MUTATED                                          2
  19P LOSS WILD-TYPE                                        7
D74V8, multiclass
                                                                   clus
vv                                                                  19P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            9
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          36
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               28
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  19P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             56
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           121
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 41
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  44
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     2  98
  19P LOSS WILD-TYPE   4 291
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   98
  19P LOSS WILD-TYPE    4  291
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 2                  4
  YES               98                291
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    83   1   6   3
  19P LOSS WILD-TYPE 235  15  12  22
D74V10, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               83                235
  R1                1                 15
  R2                6                 12
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED      26                         3
  19P LOSS WILD-TYPE    62                         3
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           1    55
  19P LOSS WILD-TYPE                                         0   188
D74V12, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                                   26                 62
  BLACK OR AFRICAN AMERICAN                                3                  3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   55                188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    48  24
  19Q LOSS WILD-TYPE 194  98
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                72                292 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                24                 98 
$`19Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-6565 TCGA-BR-7704 TCGA-BR-7723 TCGA-BR-8060 TCGA-BR-8077 
        6.61         0.62        35.24        18.54         1.32         0.69 
TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8678 TCGA-BR-A4CS 
        0.26         1.55        14.04        14.79        11.54         0.92 
TCGA-BR-A4PD TCGA-BR-A4PF TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8527 
       20.65         1.15         3.25        13.15         0.07         0.07 
TCGA-CD-A486 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 
        6.35         0.13         0.13         0.10        20.02         7.99 
TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-5724 TCGA-CG-5725 
        4.01        29.98        19.07        18.97        12.03        15.02 
TCGA-CG-5732 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8573 
       55.04         4.14        15.22        12.79        11.31        19.50 
TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-5647 TCGA-FP-8099 TCGA-FP-8631 
       11.31         2.96        15.65         0.62        17.06         0.56 
TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4H4 
        5.92        12.59        11.77         8.98         6.25        17.69 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A6RO TCGA-IN-A6RS 
       12.30         9.67        27.42        18.38         1.41         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-RD-A7BW TCGA-RD-A8MW 
        5.56         1.81         5.56        28.90         4.67        37.91 
TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8PK TCGA-VQ-A8PM 
       37.74         5.46        13.02        31.10        17.85         1.87 
TCGA-VQ-A8PU TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       23.57         8.58        44.25         8.61        21.11         0.79 

$`19Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
       32.78        13.84        13.22        16.14         1.25         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
       21.11        30.90        31.20        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       24.76        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       12.43         0.95         0.69        12.76        18.71        17.49 
TCGA-BR-8059 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 
        0.82        12.26         0.49        20.55         0.72         0.26 
TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 
       12.95        16.31         1.48         7.40         6.18        19.50 
TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 
        0.36         0.26        22.19         2.96         0.95        13.74 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 
        4.31         3.32         0.36        19.17         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39         0.72         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 
        7.53         0.49        15.81        16.44         0.59        15.68 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 
        0.62        10.68        12.56         1.15         0.66         3.02 
TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J1 
       22.26        13.41        13.51        12.89         0.79         0.72 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 
       14.17         0.53        12.82         0.66        19.36        13.51 
TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QI TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.46        20.42        13.64        11.57         5.13         2.83 
TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8528 
       13.18         0.30         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        0.13         0.16         0.10         0.10         0.13         0.13 
TCGA-CD-8536 TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         0.13         0.13         0.07         0.10         0.10 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4438 
        3.02        27.02        15.95         1.02         8.05        54.08 
TCGA-CG-4441 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 
       14.01        47.05        12.03        21.99         9.01         7.07 
TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 
       12.00        22.98        30.97         6.97         1.02         1.02 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5726 TCGA-CG-5727 
        0.99         6.02         0.99       105.07        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       65.10         4.01        21.07         7.99        12.36        12.66 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       11.93        19.13        20.55        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 
       17.85         5.95        17.19        15.98        10.55        12.33 
TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-8578 
       24.72        16.80        17.19         0.23         6.97        21.14 
TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY 
       20.91        14.27        16.44         5.92        15.16        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A748 
       14.76        13.71        11.24        11.44         9.76         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.40         7.13         7.79        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27         8.12         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A4BF TCGA-FP-A8CX 
       22.29        59.54         5.03        13.58         1.55         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-8602 
       18.08        26.47         1.51        14.27        14.17        11.41 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 
       12.10        10.62         0.76        24.30         5.59        12.30 
TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GJ 
       11.84        24.20         3.25        22.75        25.81        21.37 
TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 
       29.98         0.10         6.51        10.19         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 
       12.95        19.36         8.88         8.81        21.21         3.45 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP 
       18.81         3.39         5.36         5.19        13.08         6.44 
TCGA-IN-A6RR TCGA-IP-7968 TCGA-KB-A6F7 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 
        6.74         2.53        60.56         3.72        19.73         4.31 
TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
       11.05         8.61        16.67       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB 
      116.38        71.38        57.44         8.94        35.61        16.87 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DV TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.79         0.92        13.25        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ 
        7.73        19.07        33.63        46.26        16.31         2.70 
TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY 
        9.27        23.41        15.65        19.30        64.57        14.33 
TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       59.18        28.70        11.70         8.68        49.25        20.81 
TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91Y TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 
        1.71         7.36         9.73        55.43         4.54         6.58 
TCGA-VQ-A928 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-ZA-A8F6 
        5.72        40.08        29.98         4.21 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             55.04             122.30 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            10.490             11.885 
[1] "0.1 - 55.0 (10.5)"  "0.1 - 122.3 (11.9)"
[1] "hr=" "1.1"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         0        4       10        6         9         8
  19Q LOSS WILD-TYPE       2        9       29       25        27        41
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           0         14         11          5        8
  19Q LOSS WILD-TYPE         3         63         44         32       29
D75V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  4                  9
  STAGE IB                 10                 29
  STAGE II                  6                 25
  STAGE IIA                 9                 27
  STAGE IIB                 8                 41
  STAGE III                 0                  3
  STAGE IIIA               14                 63
  STAGE IIIB               11                 44
  STAGE IIIC                5                 32
  STAGE IV                  8                 29
[1] 11  2
[1] TRUE
[1] "dimension of 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     5  19  34  17
  19Q LOSS WILD-TYPE  16  68 139  87
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                5                 16
  T2               19                 68
  T3               34                139
  T4               17                 87
[1] 4 2
[1] TRUE
[1] "dimension of 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   27 17 14 17
  19Q LOSS WILD-TYPE 95 90 61 62
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               27                 95
  N1               17                 90
  N2               14                 61
  N3               17                 62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  19Q LOSS MUTATED    69   5   3
  19Q LOSS WILD-TYPE 284  19  15
D75V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               69                284
  M1                5                 19
  MX                3                 15
[1] 3 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    28  49
  19Q LOSS WILD-TYPE 123 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     28   49
  19Q LOSS WILD-TYPE  123  195
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               28                123
  MALE                 49                195
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  19Q LOSS MUTATED                                       6
  19Q LOSS WILD-TYPE                                    59
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                       27
  19Q LOSS WILD-TYPE                                                    130
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                                  19
  19Q LOSS WILD-TYPE                                                                50
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  19Q LOSS MUTATED                                                 17
  19Q LOSS WILD-TYPE                                               47
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  19Q LOSS MUTATED                                                          2
  19Q LOSS WILD-TYPE                                                       19
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  19Q LOSS MUTATED                                                           4
  19Q LOSS WILD-TYPE                                                         4
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  19Q LOSS MUTATED                                          2
  19Q LOSS WILD-TYPE                                        7
D75V8, multiclass
                                                                   clus
vv                                                                  19Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          27
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               19
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                17
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         2
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         2
                                                                   clus
vv                                                                  19Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           130
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 50
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  47
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          19
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          4
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           7
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  76
  19Q LOSS WILD-TYPE   5 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   76
  19Q LOSS WILD-TYPE    5  313
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 1                  5
  YES               76                313
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    65   0   4   3
  19Q LOSS WILD-TYPE 253  16  14  22
D75V10, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               65                253
  R1                0                 16
  R2                4                 14
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  19Q LOSS MUTATED      21                         2
  19Q LOSS WILD-TYPE    67                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           0    41
  19Q LOSS WILD-TYPE                                         1   202
D75V12, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                                   21                 67
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   41                202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     8  10
  20P LOSS WILD-TYPE 234 112
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                346 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                10                112 
$`20P LOSS MUTATED`
TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6564 TCGA-BR-8289 TCGA-BR-A4PD TCGA-CG-4301 
        6.18        10.13         0.82         0.26        20.65         3.02 
TCGA-D7-6519 TCGA-D7-8575 TCGA-D7-8576 TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-HU-8249 
       20.55         0.23         6.97         0.62        16.24        14.17 
TCGA-IN-A6RJ TCGA-IN-A6RO TCGA-IP-7968 TCGA-VQ-A8DU TCGA-VQ-A8PY TCGA-VQ-AA68 
        5.36         1.41         2.53         5.46        14.33        40.08 

$`20P LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       18.35        30.90         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 
       13.12        13.68         7.00        39.12         0.62        32.78 
TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6801 
       13.84        13.22        16.14         1.25         8.98        21.11 
TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7703 
       30.90        31.20        32.94        12.82         9.21        24.76 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7722 
       35.24        23.93        15.42        28.01         0.69         0.16 
TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 
       18.54        12.43         0.95         0.69        12.76        18.71 
TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8080 
       17.49         0.82         1.32         0.69        12.26         0.49 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8295 
       20.55         0.72         0.26        12.95        16.31         1.55 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.48         7.40         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
       22.19         2.96         0.95        13.74         4.31        14.04 
TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 
        3.32         0.36        19.17        14.79         0.69         0.26 
TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 
       15.85         3.72         5.39         0.72         9.21        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8683 
        7.53         0.49        11.54        15.81        16.44         0.59 
TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 
       15.68         0.62        10.68        12.56         1.15         0.66 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
        3.02        22.26         0.92        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       19.36        13.51         0.46        20.42         1.15        13.64 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.30         0.07         0.07         0.07         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.10         0.13         0.16         0.10         0.10         0.13 
TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
        0.13         0.10         6.35         0.13         0.13         0.13 
TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 
        0.13         0.07         0.10         0.10         0.10        20.02 
TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 
       27.02        15.95         1.02         7.99         8.05        54.08 
TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 TCGA-CG-4455 
        4.01        14.01        29.98        47.05        19.07        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 
       21.99         9.01        18.97         7.07        12.00        22.98 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 
       30.97         6.97         1.02         1.02         0.99         6.02 
TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5727 
        0.99       105.07        12.03        15.02        28.96        79.07 
TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 
       65.10         4.01        55.04        21.07         7.99        12.36 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        11.93        19.13        18.84        18.54        18.61 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 
       17.85         5.95        17.19         4.14        15.22        15.98 
TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 
       12.79        10.55        11.31        12.33        24.72        16.80 
TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YU 
       19.50        17.19        21.14        20.91        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV 
        5.92        15.16        13.78        14.76        13.71        11.24 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 
       11.31        11.44         9.76         2.96        15.65         4.34 
TCGA-D7-A74A TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6177 TCGA-F1-6874 TCGA-F1-6875 
        7.40         7.13         7.79         6.58        14.47        72.23 
TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 TCGA-FP-7998 
       21.27         8.12         0.39        19.53         3.02        22.29 
TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       17.06        59.54         5.03        13.58         0.56         1.55 
TCGA-FP-A8CX TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 
        0.23        18.08        26.47         1.51         5.92        14.27 
TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       12.59        11.41        12.10        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD 
        5.59        12.30        11.84        24.20         3.25        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ 
       25.81        11.77        21.37        29.98         8.98         0.10 
TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 
        6.51         6.25        10.19         0.26         2.10        12.95 
TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB 
       19.36        17.69        12.30         9.67         8.88         8.81 
TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI 
       27.42        21.21         3.45        18.81         3.39        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NT 
        5.19        13.08         6.44         6.74         6.87         5.56 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A5UG TCGA-MX-A5UJ 
        1.81         5.56        60.56        28.90         3.72        19.73 
TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8MV 
        4.31        11.05         8.61         4.67        16.67       122.30 
TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 
       37.91        40.64       115.69       116.38        71.38        57.44 
TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT 
        8.94        35.61        16.87         5.79         0.92        37.74 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       13.25        13.02        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ 
        7.73        19.07        33.63        46.26        16.31         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT 
       17.85         1.87         9.27        23.41        15.65        19.30 
TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
       23.57        64.57        59.18        28.70        11.70         8.68 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y 
       49.25        20.81         1.71         7.36         8.58         9.73 
TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 
       44.25         8.61        55.43         4.54         6.58         5.72 
TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       29.98        21.11         4.21         0.79 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.23               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             40.08             122.30 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             5.820             11.805 
[1] "0.2 - 40.1 (5.8)"   "0.1 - 122.3 (11.8)"
[1] "hr=" "2.3"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         0        1        3        0         0         2
  20P LOSS WILD-TYPE       2       12       36       31        36        47
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           0          4          5          1        4
  20P LOSS WILD-TYPE         3         73         50         36       33
D76V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  1                 12
  STAGE IB                  3                 36
  STAGE II                  0                 31
  STAGE IIA                 0                 36
  STAGE IIB                 2                 47
  STAGE III                 0                  3
  STAGE IIIA                4                 73
  STAGE IIIB                5                 50
  STAGE IIIC                1                 36
  STAGE IV                  4                 33
[1] 11  2
[1] TRUE
[1] "dimension of 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     2   4   8   6
  20P LOSS WILD-TYPE  19  83 165  98
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                2                 19
  T2                4                 83
  T3                8                165
  T4                6                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P LOSS MUTATED     5   4   6   5
  20P LOSS WILD-TYPE 117 103  69  74
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                5                117
  N1                4                103
  N2                6                 69
  N3                5                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  20P LOSS MUTATED    14   3   3
  20P LOSS WILD-TYPE 339  21  15
D76V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0               14                339
  M1                3                 21
  MX                3                 15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    11   9
  20P LOSS WILD-TYPE 140 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     11    9
  20P LOSS WILD-TYPE  140  235
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               11                140
  MALE                  9                235
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  20P LOSS MUTATED                                       2
  20P LOSS WILD-TYPE                                    63
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                       10
  20P LOSS WILD-TYPE                                                    147
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                                   1
  20P LOSS WILD-TYPE                                                                68
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  20P LOSS MUTATED                                                  6
  20P LOSS WILD-TYPE                                               58
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  20P LOSS MUTATED                                                          1
  20P LOSS WILD-TYPE                                                       20
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  20P LOSS MUTATED                                                           0
  20P LOSS WILD-TYPE                                                         8
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  20P LOSS MUTATED                                          0
  20P LOSS WILD-TYPE                                        9
D76V8, multiclass
                                                                   clus
vv                                                                  20P LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            2
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          10
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                1
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 6
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         1
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        0
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         0
                                                                   clus
vv                                                                  20P LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             63
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           147
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 68
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  58
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          20
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          8
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           9
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  18
  20P LOSS WILD-TYPE   4 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   18
  20P LOSS WILD-TYPE    4  371
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 2                  4
  YES               18                371
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    16   1   2   1
  20P LOSS WILD-TYPE 302  15  16  24
D76V10, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               16                302
  R1                1                 15
  R2                2                 16
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  20P LOSS MUTATED       2                         0
  20P LOSS WILD-TYPE    86                         6
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           0    15
  20P LOSS WILD-TYPE                                         1   228
D76V12, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                                    2                 86
  BLACK OR AFRICAN AMERICAN                                0                  6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                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"

Clustering(77) Variable = 21Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    96  47
  21Q LOSS WILD-TYPE 146  75
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               143                221 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                47                 75 
$`21Q LOSS MUTATED`
TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
       11.70         6.97        18.35        13.68         7.00         0.82 
TCGA-BR-6565 TCGA-BR-6803 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 
        0.62        31.20        35.24        15.42        28.01        18.54 
TCGA-BR-7959 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 
       18.71         0.82         1.32         0.49         0.72        16.31 
TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8361 TCGA-BR-8365 TCGA-BR-8368 TCGA-BR-8369 
        1.48         7.40        19.50         2.96         4.31        14.04 
TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8683 
       14.79         5.39         0.72         9.21        11.54         0.59 
TCGA-BR-8686 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 
       15.68        10.68         0.66        22.26         0.92         0.72 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI 
       13.51         0.46        20.65        20.42         1.15        13.64 
TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8530 TCGA-CD-8535 
        0.07         0.07         0.07         0.10         0.16         0.13 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4438 
        0.13         0.13         0.13         0.10        20.02        54.08 
TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4455 TCGA-CG-4466 TCGA-CG-4475 TCGA-CG-4477 
        4.01        47.05        12.03        18.97        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5728 TCGA-CG-5730 
        6.97         1.02        12.03        15.02        65.10         4.01 
TCGA-CG-5732 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 
       55.04        11.93        19.13         5.95        17.19        15.98 
TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX 
       12.79        11.31         6.97        21.14        16.44        11.31 
TCGA-D7-A6F2 TCGA-D7-A74A TCGA-EQ-5647 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7829 
       15.65         7.40         0.62        72.23         8.12        19.53 
TCGA-FP-8099 TCGA-FP-A8CX TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8249 TCGA-HU-8604 
       17.06         0.23        26.47         1.51        14.17        12.10 
TCGA-HU-A4G8 TCGA-HU-A4GC TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H3 
       11.84         3.25         8.98         6.25         0.26        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 
       17.69        12.30         9.67        21.21        18.81         3.39 
TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RR TCGA-IN-A7NT 
       18.38         5.36         5.19         1.41         6.74         5.56 
TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A663 
        1.81         2.53         5.56        60.56        28.90         4.31 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 
      122.30        37.91       115.69        57.44         8.94        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DV TCGA-VQ-A8P5 TCGA-VQ-A8PK 
        5.79         0.92        37.74        13.25         7.73        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A8PU TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A91A 
        1.87        23.41        23.57        64.57        14.33        28.70 
TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A924 
       49.25        20.81         1.71         9.73        44.25        55.43 
TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZQ-A9CR 
        4.54        40.08        29.98        21.11         0.79 

$`21Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4201 TCGA-BR-4267 
        5.62         6.61         4.64         7.43        30.90         6.18 
TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6456 
        9.57         6.61        34.68        15.95        13.12        10.13 
TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
       39.12        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7197 
        8.98        21.11        30.90        32.94        12.82         9.21 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7851 TCGA-BR-7901 
       24.76        23.93         0.69         0.16        12.43         0.95 
TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8077 TCGA-BR-8078 TCGA-BR-8081 
        0.69        12.76        17.49         0.69        12.26        20.55 
TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8360 TCGA-BR-8362 
        0.26        12.95         0.26         1.55         6.18         0.36 
TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8370 TCGA-BR-8371 
        0.26        22.19         0.95        13.74         3.32         0.36 
TCGA-BR-8372 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8486 
       19.17         0.69         0.26        15.85         3.72        20.22 
TCGA-BR-8487 TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
        1.12        12.79        15.81         2.14        13.45         0.20 
TCGA-BR-8676 TCGA-BR-8677 TCGA-BR-8680 TCGA-BR-8682 TCGA-BR-8687 TCGA-BR-A44T 
        7.53         0.49        15.81        16.44         0.62        12.56 
TCGA-BR-A44U TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ 
        1.15         3.02        13.41        13.51        12.89         0.79 
TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4QL 
       14.17         0.53        12.82         0.66        19.36        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
        5.13         2.83         3.25        13.15        13.18         0.30 
TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 
        0.07         0.07         0.13         0.10         0.10         0.13 
TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ 
        0.10         6.35         0.13         0.07         0.10         0.10 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4437 
        3.02        27.02        15.95         1.02         7.99         8.05 
TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4469 
       14.01        29.98        19.07        21.99         9.01         7.07 
TCGA-CG-4472 TCGA-CG-5718 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
       12.00         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
       28.96        79.07        21.07         7.99        12.36        12.66 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6527 
       20.55        18.84        18.54        18.61        17.85         4.14 
TCGA-D7-6528 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 
       15.22        10.55        12.33        24.72        16.80        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV TCGA-D7-A4YX 
       17.19         0.23        20.91        14.27         5.92        15.16 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6EZ 
       13.78        14.76        13.71        11.24        11.44         9.76 
TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 
        2.96         4.34         7.13         7.79        16.24         6.58 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-7735 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 
       14.47        21.27         0.39         3.02        22.29        59.54 
TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HU-8243 
        5.03        13.58         0.56         1.55        18.08         5.92 
TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 
       14.27        12.59        11.41        10.62         0.76        24.30 
TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G9 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH 
        5.59        12.30        24.20        22.75        25.81        11.77 
TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H0 
       21.37        29.98         0.10         6.51        10.19         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 TCGA-IN-A6RN 
       12.95         8.88         8.81        27.42         3.45        13.08 
TCGA-IN-A6RP TCGA-IN-A6RS TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BT 
        6.44         6.87         3.72        19.73        11.05         8.61 
TCGA-RD-A7BW TCGA-RD-A7C1 TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8NB 
        4.67        16.67        40.64       116.38        71.38        16.87 
TCGA-VQ-A8DU TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        5.46        13.02        31.10        21.73        22.36        23.77 
TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO 
       19.07        33.63        46.26        16.31         2.70         9.27 
TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91W 
       15.65        19.30        59.18        11.70         8.68         7.36 
TCGA-VQ-A91X TCGA-VQ-A922 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-ZA-A8F6 
        8.58         8.61         6.58         5.72         4.21 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.07               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            122.30             116.38 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             11.84              11.44 
[1] "0.1 - 122.3 (11.8)" "0.1 - 116.4 (11.4)"
[1] "hr=" "1.1"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         0        3       18        8        16        18
  21Q LOSS WILD-TYPE       2       10       21       23        20        31
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           1         38         21         14       11
  21Q LOSS WILD-TYPE         2         39         34         23       26
D77V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  3                 10
  STAGE IB                 18                 21
  STAGE II                  8                 23
  STAGE IIA                16                 20
  STAGE IIB                18                 31
  STAGE III                 1                  2
  STAGE IIIA               38                 39
  STAGE IIIB               21                 34
  STAGE IIIC               14                 23
  STAGE IV                 11                 26
[1] 11  2
[1] TRUE
[1] "dimension of 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     5  36  73  35
  21Q LOSS WILD-TYPE  16  51 100  69
D77V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                5                 16
  T2               36                 51
  T3               73                100
  T4               35                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  21Q LOSS MUTATED   43 44 33 30
  21Q LOSS WILD-TYPE 79 63 42 49
D77V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               43                 79
  N1               44                 63
  N2               33                 42
  N3               30                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  21Q LOSS MUTATED   141   5   8
  21Q LOSS WILD-TYPE 212  19  10
D77V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0              141                212
  M1                5                 19
  MX                8                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    64  90
  21Q LOSS WILD-TYPE  87 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     64   90
  21Q LOSS WILD-TYPE   87  154
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               64                 87
  MALE                 90                154
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  21Q LOSS MUTATED                                      21
  21Q LOSS WILD-TYPE                                    44
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                       59
  21Q LOSS WILD-TYPE                                                     98
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                                  32
  21Q LOSS WILD-TYPE                                                                37
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  21Q LOSS MUTATED                                                 28
  21Q LOSS WILD-TYPE                                               36
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  21Q LOSS MUTATED                                                          9
  21Q LOSS WILD-TYPE                                                       12
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  21Q LOSS MUTATED                                                           1
  21Q LOSS WILD-TYPE                                                         7
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  21Q LOSS MUTATED                                          3
  21Q LOSS WILD-TYPE                                        6
D77V8, multiclass
                                                                   clus
vv                                                                  21Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           21
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          59
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               32
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                28
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         3
                                                                   clus
vv                                                                  21Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             44
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                            98
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 37
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  36
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          12
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           6
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4 150
  21Q LOSS WILD-TYPE   2 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4  150
  21Q LOSS WILD-TYPE    2  239
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 4                  2
  YES              150                239
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED   129   6   6   8
  21Q LOSS WILD-TYPE 189  10  12  17
D77V10, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              129                189
  R1                6                 10
  R2                6                 12
  RX                8                 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"
D77V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  21Q LOSS MUTATED      31                         2
  21Q LOSS WILD-TYPE    57                         4
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           0    95
  21Q LOSS WILD-TYPE                                         1   148
D77V12, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                                   31                 57
  BLACK OR AFRICAN AMERICAN                                2                  4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   95                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"

Clustering(78) Variable = 22Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    74  41
  22Q LOSS WILD-TYPE 168  81
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               115                249 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                41                 81 
$`22Q LOSS MUTATED`
TCGA-BR-4183 TCGA-BR-4267 TCGA-BR-6456 TCGA-BR-6458 TCGA-BR-6564 TCGA-BR-6565 
        6.61         6.18        10.13         7.00         0.82         0.62 
TCGA-BR-6709 TCGA-BR-7197 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-8058 TCGA-BR-8059 
        1.25         9.21        15.42        28.01        17.49         0.82 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8080 TCGA-BR-8297 TCGA-BR-8369 TCGA-BR-8484 
        1.32         0.69         0.49         7.40        14.04         0.72 
TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-8690 
        0.49        11.54        16.44         0.59         0.62        10.68 
TCGA-BR-A4CQ TCGA-BR-A4J1 TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PF TCGA-BR-A4QI 
       22.26         0.72        19.36        20.65         1.15        13.64 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8530 
       13.15         0.30         0.07         0.07         0.07         0.16 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A48C 
        0.13         6.35         0.13         0.13         0.13         0.13 
TCGA-CD-A4MH TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4444 TCGA-CG-4460 
        0.10         8.05        54.08         4.01        47.05        21.99 
TCGA-CG-4466 TCGA-CG-4477 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5732 TCGA-D7-5578 
       18.97        30.97        12.03        15.02        55.04        12.66 
TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-6820 
       11.93        20.55         4.14        15.22        12.79        11.31 
TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8578 TCGA-D7-A4YU TCGA-D7-A6EX TCGA-D7-A6F2 
       19.50         0.23        21.14        16.44        11.31        15.65 
TCGA-D7-A74A TCGA-EQ-5647 TCGA-EQ-A4SO TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8631 
        7.40         0.62        16.24        19.53        17.06         0.56 
TCGA-FP-A4BF TCGA-HU-8243 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GP TCGA-HU-A4GY 
        1.55         5.92        14.17        22.75         8.98         0.26 
TCGA-HU-A4H0 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4HD TCGA-IN-8663 TCGA-IN-A6RI 
        2.10        17.69         9.67        27.42         3.39        18.38 
TCGA-IN-A6RJ TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NU TCGA-IP-7968 
        5.36        13.08         6.44         6.74         1.81         2.53 
TCGA-KB-A6F5 TCGA-MX-A663 TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8N1 TCGA-RD-A8N9 
        5.56         4.31         8.61        16.67       115.69        35.61 
TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
        5.79         0.92        37.74         5.46        13.25        13.02 
TCGA-VQ-A8PC TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PU TCGA-VQ-A8PY TCGA-VQ-A91A 
       46.26        17.85         1.87        23.57        14.33        28.70 
TCGA-VQ-A91Q TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A925 TCGA-VQ-AA6B 
       20.81         1.71         8.58         9.73         4.54        29.98 
TCGA-ZQ-A9CR 
        0.79 

$`22Q LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4191 
        5.62        11.70         6.97         4.64         7.43        18.35 
TCGA-BR-4201 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 
       30.90         9.57         6.61        34.68        15.95        13.12 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 
       13.68        39.12        32.78        13.84        13.22        16.14 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7723 
       24.76        35.24        23.93         0.69         0.16        18.54 
TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8078 
       12.43         0.95         0.69        12.76        18.71        12.26 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 
       20.55         0.72         0.26        12.95         0.26        16.31 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8363 
        1.55         1.48         6.18        19.50         0.36         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8370 
       22.19         2.96         0.95        13.74         4.31         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8588 
        3.72         5.39         9.21        20.22         1.12        12.79 
TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 TCGA-BR-8680 
       15.81         2.14        13.45         0.20         7.53        15.81 
TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A44U TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CS 
       15.68        12.56         1.15         0.66         3.02         0.92 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J4 
       13.41        13.51        12.89         0.79        14.17         0.53 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PE TCGA-BR-A4QL 
       12.82         0.66        13.51         0.46        20.42        11.57 
TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5803 TCGA-CD-8525 
        5.13         2.83         3.25        13.18         0.07         0.07 
TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8535 TCGA-CD-8536 
        0.10         0.13         0.10         0.10         0.13         0.10 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 
        0.07         0.10         0.10        20.02         3.02        27.02 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4436 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
       15.95         1.02         7.99        14.01        29.98        19.07 
TCGA-CG-4455 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-5717 
       12.03         9.01         7.07        12.00        22.98         6.97 
TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        1.02         1.02         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 
       28.96        79.07        65.10         4.01        21.07         7.99 
TCGA-D7-5577 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 
       12.36        19.13        18.84        18.54        18.61        17.85 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8570 
        5.95        17.19        15.98        10.55        12.33        24.72 
TCGA-D7-8572 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8579 TCGA-D7-A4YT TCGA-D7-A4YV 
       16.80        17.19         6.97        20.91        14.27         5.92 
TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY 
       15.16        13.78        14.76        13.71        11.24        11.44 
TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A748 TCGA-D7-A74B TCGA-EQ-8122 TCGA-F1-6177 
        9.76         2.96         4.34         7.13         7.79         6.58 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7916 
       14.47        72.23        21.27         8.12         0.39         3.02 
TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8211 TCGA-FP-A8CX TCGA-HF-A5NB 
       22.29        59.54         5.03        13.58         0.23        18.08 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8245 TCGA-HU-8602 TCGA-HU-8604 
       26.47         1.51        14.27        12.59        11.41        12.10 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 
       10.62         0.76        24.30         5.59        12.30        11.84 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.20         3.25        25.81        11.77        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H3 
        0.10         6.51         6.25        10.19        12.95        19.36 
TCGA-HU-A4H5 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 
       12.30         8.88         8.81        21.21         3.45        18.81 
TCGA-IN-A6RL TCGA-IN-A6RO TCGA-IN-A6RS TCGA-IN-A7NT TCGA-KB-A6F7 TCGA-KB-A93H 
        5.19         1.41         6.87         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8MW 
        3.72        19.73        11.05         4.67       122.30        37.91 
TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8NB 
       40.64       116.38        71.38        57.44         8.94        16.87 
TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 
       31.10        21.73        22.36        23.77         7.73        19.07 
TCGA-VQ-A8PB TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       33.63        16.31         2.70         9.27        23.41        15.65 
TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PZ TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       19.30        64.57        59.18        11.70         8.68        49.25 
TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A928 
        7.36        44.25         8.61        55.43         6.58         5.72 
TCGA-VQ-AA68 TCGA-VQ-AA6J TCGA-ZA-A8F6 
       40.08        21.11         4.21 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.07               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            115.69             122.30 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              8.98              12.30 
[1] "0.1 - 115.7 (9.0)"  "0.1 - 122.3 (12.3)"
[1] "hr=" "1.3"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         0        0       14       11        11        15
  22Q LOSS WILD-TYPE       2       13       25       20        25        34
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           1         30         18         11       11
  22Q LOSS WILD-TYPE         2         47         37         26       26
D78V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   0                  2
  STAGE IA                  0                 13
  STAGE IB                 14                 25
  STAGE II                 11                 20
  STAGE IIA                11                 25
  STAGE IIB                15                 34
  STAGE III                 1                  2
  STAGE IIIA               30                 47
  STAGE IIIB               18                 37
  STAGE IIIC               11                 26
  STAGE IV                 11                 26
[1] 11  2
[1] TRUE
[1] "dimension of 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     4  27  64  28
  22Q LOSS WILD-TYPE  17  60 109  76
D78V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                4                 17
  T2               27                 60
  T3               64                109
  T4               28                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  22Q LOSS MUTATED   34 31 29 28
  22Q LOSS WILD-TYPE 88 76 46 51
D78V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               34                 88
  N1               31                 76
  N2               29                 46
  N3               28                 51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  22Q LOSS MUTATED   114   5   6
  22Q LOSS WILD-TYPE 239  19  12
D78V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0              114                239
  M1                5                 19
  MX                6                 12
[1] 3 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
  22Q LOSS MUTATED    47  78
  22Q LOSS WILD-TYPE 104 166
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     47   78
  22Q LOSS WILD-TYPE  104  166
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               47                104
  MALE                 78                166
[1] 2 2
[1] FALSE
                    vv
clus                 STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  22Q LOSS MUTATED                                      16
  22Q LOSS WILD-TYPE                                    49
                    vv
clus                 STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                       49
  22Q LOSS WILD-TYPE                                                    108
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                                  21
  22Q LOSS WILD-TYPE                                                                48
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  22Q LOSS MUTATED                                                 25
  22Q LOSS WILD-TYPE                                               39
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  22Q LOSS MUTATED                                                          8
  22Q LOSS WILD-TYPE                                                       13
                    vv
clus                 STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  22Q LOSS MUTATED                                                           2
  22Q LOSS WILD-TYPE                                                         6
                    vv
clus                 STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  22Q LOSS MUTATED                                          4
  22Q LOSS WILD-TYPE                                        5
D78V8, multiclass
                                                                   clus
vv                                                                  22Q LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           16
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          49
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               21
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                25
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         8
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                        2
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                         4
                                                                   clus
vv                                                                  22Q LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                             49
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                           108
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                 48
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                  39
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                          13
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                          6
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                           5
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     4 121
  22Q LOSS WILD-TYPE   2 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4  121
  22Q LOSS WILD-TYPE    2  268
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 4                  2
  YES              121                268
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    97   7   8   6
  22Q LOSS WILD-TYPE 221   9  10  19
D78V10, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               97                221
  R1                7                  9
  R2                8                 10
  RX                6                 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"
D78V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN
  22Q LOSS MUTATED      29                         1
  22Q LOSS WILD-TYPE    59                         5
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           1    77
  22Q LOSS WILD-TYPE                                         0   166
D78V12, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                                   29                 59
  BLACK OR AFRICAN AMERICAN                                1                  5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   77                166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = XQ LOSS MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    28  11
  XQ LOSS WILD-TYPE 214 111
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               39               325 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               11               111 
$`XQ LOSS MUTATED`
TCGA-BR-4191 TCGA-BR-7197 TCGA-BR-8291 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8678 
       18.35         9.21        16.31        19.50         0.36        11.54 
TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4QI TCGA-CD-8524 
       15.81         1.15        22.26         0.92        13.64         0.07 
TCGA-CD-8535 TCGA-CD-A489 TCGA-CG-4300 TCGA-CG-4443 TCGA-CG-4444 TCGA-CG-4449 
        0.13         0.13        20.02        29.98        47.05        19.07 
TCGA-CG-4469 TCGA-CG-5725 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6817 TCGA-D7-6822 
        7.07        15.02        11.93        20.55        12.79        12.33 
TCGA-D7-8575 TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A74A TCGA-FP-8211 TCGA-FP-A4BF 
        0.23        11.31         9.76         7.40        13.58         1.55 
TCGA-HU-8604 TCGA-HU-A4H5 TCGA-IN-7806 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RP 
       12.10        12.30        21.21         3.39        18.38         6.44 
TCGA-IN-A6RR TCGA-VQ-A8PU TCGA-VQ-AA68 
        6.74        23.57        40.08 

$`XQ LOSS WILD-TYPE`
TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
        5.62        11.70         6.61         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6453 
       30.90         6.18         9.57         6.61        34.68        15.95 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.12        10.13        13.68         7.00        39.12         0.82 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 
        0.62        32.78        13.84        13.22        16.14         1.25 
TCGA-BR-6710 TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6803 TCGA-BR-6852 TCGA-BR-7196 
        8.98        21.11        30.90        31.20        32.94        12.82 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 
       24.76        35.24        23.93        15.42        28.01         0.69 
TCGA-BR-7722 TCGA-BR-7723 TCGA-BR-7851 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 
        0.16        18.54        12.43         0.95         0.69        12.76 
TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8078 
       18.71        17.49         0.82         1.32         0.69        12.26 
TCGA-BR-8080 TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8289 
        0.49        20.55         0.72         0.26        12.95         0.26 
TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 
        1.55         1.48         7.40         6.18         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 TCGA-BR-8370 
        2.96         0.95        13.74         4.31        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8373 TCGA-BR-8380 TCGA-BR-8381 TCGA-BR-8382 
        0.36        19.17        14.79         0.69         0.26        15.85 
TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 
        3.72         5.39         0.72         9.21        20.22         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        15.81         2.14        13.45         0.20         7.53 
TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-8690 
        0.49        16.44         0.59        15.68         0.62        10.68 
TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IY 
       12.56         0.66         3.02        13.41        13.51        12.89 
TCGA-BR-A4IZ TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J6 
        0.79         0.72        14.17         0.53        12.82         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF 
       19.36        13.51         0.46        20.65        20.42         1.15 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       11.57         5.13         2.83         3.25        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8528 
        0.30         0.07         0.07         0.07         0.07         0.10 
TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8536 
        0.13         0.16         0.10         0.10         0.13         0.10 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A48A TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MH 
        6.35         0.13         0.13         0.13         0.07         0.10 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 
        0.10         0.10         3.02        27.02        15.95         1.02 
TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4455 
        7.99         8.05        54.08         4.01        14.01        12.03 
TCGA-CG-4460 TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4475 TCGA-CG-4477 
       21.99         9.01        18.97        12.00        22.98        30.97 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97         1.02         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5727 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        28.96        79.07        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6518 
       55.04        21.07         7.99        12.36        12.66        19.13 
TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 
       18.84        18.54        18.61        17.85         5.95        17.19 
TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8570 
        4.14        15.22        15.98        10.55        11.31        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-8579 
       16.80        19.50        17.19         6.97        21.14        20.91 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.27        16.44         5.92        15.16        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EV TCGA-D7-A6EY TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-D7-A748 
       13.71        11.24        11.44         2.96        15.65         4.34 
TCGA-D7-A74B TCGA-EQ-5647 TCGA-EQ-8122 TCGA-EQ-A4SO TCGA-F1-6177 TCGA-F1-6874 
        7.13         0.62         7.79        16.24         6.58        14.47 
TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 TCGA-FP-7916 
       72.23        21.27         8.12         0.39        19.53         3.02 
TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8209 TCGA-FP-8210 TCGA-FP-8631 TCGA-FP-A8CX 
       22.29        17.06        59.54         5.03         0.56         0.23 
TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8244 TCGA-HU-8245 
       18.08        26.47         1.51         5.92        14.27        12.59 
TCGA-HU-8249 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 
       14.17        11.41        10.62         0.76        24.30         5.59 
TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GD TCGA-HU-A4GF 
       12.30        11.84        24.20         3.25        22.75        25.81 
TCGA-HU-A4GH TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       11.77        21.37        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 
        6.25        10.19         0.26         2.10        12.95        19.36 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-HU-A4HD TCGA-IN-7808 
       17.69         9.67         8.88         8.81        27.42         3.45 
TCGA-IN-8462 TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RO TCGA-IN-A6RS 
       18.81         5.36         5.19        13.08         1.41         6.87 
TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H 
        5.56         1.81         2.53         5.56        60.56        28.90 
TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-MX-A663 TCGA-RD-A7BS TCGA-RD-A7BT TCGA-RD-A7BW 
        3.72        19.73         4.31        11.05         8.61         4.67 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N2 
       16.67       122.30        37.91        40.64       115.69       116.38 
TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-SW-A7EB 
       71.38        57.44         8.94        35.61        16.87         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 
        0.92        37.74         5.46        13.25        13.02        31.10 
TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       21.73        22.36        23.77         7.73        19.07        33.63 
TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PO 
       46.26        16.31         2.70        17.85         1.87         9.27 
TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       23.41        15.65        19.30        64.57        14.33        59.18 
TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A91U 
       28.70        11.70         8.68        49.25        20.81         1.71 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A924 
        7.36         8.58         9.73        44.25         8.61        55.43 
TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-AA6B TCGA-VQ-AA6J TCGA-ZA-A8F6 
        4.54         6.58         5.72        29.98        21.11         4.21 
TCGA-ZQ-A9CR 
        0.79 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            47.05            122.30 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            12.30             11.41 
[1] "0.1 - 47.0 (12.3)"  "0.1 - 122.3 (11.4)"
[1] "hr=" "1.2"
D79V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         0        1        5        4         3         4
  XQ LOSS WILD-TYPE       2       12       34       27        33        45
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           0         12          3          5        3
  XQ LOSS WILD-TYPE         3         65         52         32       34
D79V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  0                 2
  STAGE IA                 1                12
  STAGE IB                 5                34
  STAGE II                 4                27
  STAGE IIA                3                33
  STAGE IIB                4                45
  STAGE III                0                 3
  STAGE IIIA              12                65
  STAGE IIIB               3                52
  STAGE IIIC               5                32
  STAGE IV                 3                34
[1] 11  2
[1] TRUE
[1] "dimension of 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     3  11  20   7
  XQ LOSS WILD-TYPE  18  76 153  97
D79V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               3                18
  T2              11                76
  T3              20               153
  T4               7                97
[1] 4 2
[1] TRUE
[1] "dimension of 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    12  10  11   8
  XQ LOSS WILD-TYPE 110  97  64  71
D79V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              12               110
  N1              10                97
  N2              11                64
  N3               8                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  XQ LOSS MUTATED    40   1   1
  XQ LOSS WILD-TYPE 313  23  17
D79V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              40               313
  M1               1                23
  MX               1                17
[1] 3 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
  XQ LOSS MUTATED    10  32
  XQ LOSS WILD-TYPE 141 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     10   32
  XQ LOSS WILD-TYPE  141  212
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              10               141
  MALE                32               212
[1] 2 2
[1] FALSE
                   vv
clus                STOMACH  ADENOCARCINOMA  DIFFUSE TYPE
  XQ LOSS MUTATED                                       6
  XQ LOSS WILD-TYPE                                    59
                   vv
clus                STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                       18
  XQ LOSS WILD-TYPE                                                    139
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                                   4
  XQ LOSS WILD-TYPE                                                                65
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE
  XQ LOSS MUTATED                                                  9
  XQ LOSS WILD-TYPE                                               55
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE
  XQ LOSS MUTATED                                                          3
  XQ LOSS WILD-TYPE                                                       18
                   vv
clus                STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE
  XQ LOSS MUTATED                                                           1
  XQ LOSS WILD-TYPE                                                         7
                   vv
clus                STOMACH ADENOCARCINOMA  SIGNET RING TYPE
  XQ LOSS MUTATED                                          1
  XQ LOSS WILD-TYPE                                        8
D79V8, multiclass
                                                                   clus
vv                                                                  XQ LOSS MUTATED
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                           6
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                         18
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)               4
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                9
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                        3
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                       1
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                        1
                                                                   clus
vv                                                                  XQ LOSS WILD-TYPE
  STOMACH  ADENOCARCINOMA  DIFFUSE TYPE                                            59
  STOMACH  ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                          139
  STOMACH  INTESTINAL ADENOCARCINOMA  NOT OTHERWISE SPECIFIED (NOS)                65
  STOMACH  INTESTINAL ADENOCARCINOMA  TUBULAR TYPE                                 55
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240MUCINOUS TYPE                         18
  STOMACH  INTESTINAL ADENOCARCINOMA \302\240PAPILLARY TYPE                         7
  STOMACH ADENOCARCINOMA  SIGNET RING TYPE                                          8
[1] 7 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  40
  XQ LOSS WILD-TYPE   4 349
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   40
  XQ LOSS WILD-TYPE    4  349
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                2                 4
  YES              40               349
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    34   5   0   2
  XQ LOSS WILD-TYPE 284  11  18  23
D79V10, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              34               284
  R1               5                11
  R2               0                18
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN
  XQ LOSS MUTATED       7                         0
  XQ LOSS WILD-TYPE    81                         6
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           0    28
  XQ LOSS WILD-TYPE                                         1   215
D79V12, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                                   7                81
  BLACK OR AFRICAN AMERICAN                               0                 6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  28               215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
