[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"      "-oTOV-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/OV-TP/11541686/OV-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/11551024/transformed.cor.cli.txt"

nPatients in clinical file=588, in cluster file=579, common to both=571
[1]  80 571
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              167               404 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              167               404 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              218               353 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              218               353 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              183               388 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              183               388 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              152               419 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              152               419 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              160               411 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              160               411 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              271               300 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              271               300 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               59               512 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               59               512 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               32               539 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               32               539 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              195               376 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              195               376 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               59               512 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               59               512 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              166               405 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              166               405 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               97               474 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               97               474 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              178               393 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              178               393 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              198               373 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              198               373 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              117               454 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              117               454 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              239               332 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              239               332 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               88               483 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               88               483 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               43               528 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               43               528 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               185                386 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               185                386 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               108                463 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               108                463 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                76                495 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                76                495 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               112                459 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               112                459 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               253                318 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               253                318 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               175                396 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               175                396 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                59                512 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                59                512 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                58                513 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                58                513 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                39                532 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                39                532 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                59                512 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                59                512 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                31                540 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                31                540 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                549 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                22                549 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                47                524 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                47                524 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               119                452 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               119                452 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                72                499 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                72                499 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               168                403 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               168                403 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               160                411 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               160                411 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               286                285 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               286                285 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               324                247 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               324                247 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               109                462 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               109                462 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                547 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                24                547 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              105               466 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              105               466 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               64               507 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               64               507 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               43               528 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               43               528 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               53               518 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               53               518 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               59               512 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               59               512 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               93               478 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               93               478 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43               528 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               43               528 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              312               259 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              312               259 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              358               213 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              358               213 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              131               440 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              131               440 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              221               350 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              221               350 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              163               408 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              163               408 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              238               333 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              238               333 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              120               451 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              120               451 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               81               490 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               81               490 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              273               298 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              273               298 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               89               482 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               89               482 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              262               309 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              262               309 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              285               286 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              285               286 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                96                475 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                96                475 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               124                447 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               124                447 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               196                375 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               196                375 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               148                423 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               148                423 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                78                493 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                78                493 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               103                468 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               103                468 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               305                266 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               305                266 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               212                359 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               212                359 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               276                295 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               276                295 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               330                241 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               330                241 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               408                163 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               408                163 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               473                 98 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               473                 98 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               379                192 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               379                192 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               231                340 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               231                340 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               289                282 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               289                282 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               184                387 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               184                387 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               176                395 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               176                395 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                49                522 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                49                522 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                32                539 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                32                539 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               194                377 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               194                377 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               427                144 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               427                144 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              274               297 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              274               297 
[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] "KARNOFSKYPERFORMANCESCORE"                         
[15] "EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE"
[16] "HISTOLOGICALTYPE"                                  
[17] "TUMORGRADE"                                        
[18] "TUMORSTAGE"                                        
[19] "PATIENTTUMORRECURRENCESTATUS"                      
[20] "DAYSTOTUMORRECURRENCE"                             
[21] "CHEMOTHERAPY"                                      
[22] "RADIATIONS.RADIATION.REGIMENINDICATION"            
[23] "COMPLETENESS.OF.RESECTION"                         
[24] "RACE"                                              
[25] "ETHNICITY"                                         
[26] "BATCHNUMBER"                                       

Input Data has 26 rows and 571 columns.

[1] "Batch" "26"   
[1] "Last Follow UP"
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
        1224         1247           55         1495           NA         1418 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
          NA           NA           NA         1993         1919           NA 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1357 TCGA-04-1360 
          NA           NA         1991           NA           NA           NA 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
         989           NA           NA         2329         2174         2506 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
          NA         1265           NA           NA         1167           NA 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
          NA           NA           NA           NA           NA           NA 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 
        1966           NA           NA           NA           NA           NA 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
          NA           NA           NA           NA           NA           NA 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
          NA           NA           NA         1752         1882         1684 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
         928          547          178           92          260         2967 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
         188          186           NA           NA         3419         2163 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
        1919         1209          637          819          379         1652 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
         788         2478          563         1011          982          356 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
         119         1078         1089          460          604          189 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
         748         1355         1204           83          377          946 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
         462          542         1678           76          340          346 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
         351         1036          981          944          651          257 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
        1184         1117          873          923          596          265 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
         237          247          252          249         1334         1073 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
        1073          414         2097         3260         2780         2259 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
        2028         2141         1881         2068         2099         1319 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
        1748         1708         1736          589         1441         1470 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
        1455         1367         1364         1128          843         1036 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
         912          644          453          420          141          195 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
         185          331          201          224          184          180 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
         208          143          128          162         1662         2648 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
        1877          895         2982          629          681         2154 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
        2521         1595         2237         1162         1498          129 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
        1652         1144         1168          425          999          504 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
         128          134          145          127           78          119 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
          94          433          372          262          328          266 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
         191         1666           NA           NA          789          797 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
        2196          837          772          581          508           89 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
          81         1446         1294         1233          468          816 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
         966         1503          268          886          575           68 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        1562         1658           98          949         2089          139 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
        1013         2616         3953          130          194         1189 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
        1018         1768           16          759         3525         2661 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
        2788         2342         1516           84          143          137 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
         232          598          354          663         1264          233 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
         679         1646         1933         1442          192          194 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
         238          243          239           23          190          183 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
         181          163          147          529          863          583 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
         568         1324          260         2218          379         1373 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
        3224          277          105           36          676          820 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
        1746         1955          493         1721         1249         1579 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
        1259         1767         2692         2148         1213          594 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
        1341         1384         1451          787          312          524 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
        2742         2688         1470         1163          253          106 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
         113          116          133          343          176          168 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
         298          690          919          500          336         2467 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
         148         4624         1364         1769         1059         3337 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
         439         1641          562          857         1947         1354 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
        1736         1100           24           11         1446          962 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
        2143         1357           25         2049         1102          506 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
        1007         1699         1620           31          820          974 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
        1553         1126           31         1064         1977         1124 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
        1033           91          365           90          565          548 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
         481           11          627          239            9         1732 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
        1843         1081         1558          455          760          549 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
        2587          396         1492           31         1157           92 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
         365         1369          608         1278           90          883 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
         943          821         2400         1360         1435         3096 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
        1172           24         1025          949         2078           16 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
         514          568         1815          555         1277          889 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
        1053          517         2606         2032         1914         1190 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
         950          699          741          686          527          376 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
         360          374          454          255          220          163 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
        1053         2621         1977         1900         1372          149 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
        1285          360          349          297          640         1158 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
        1579         1103           75          477            8         1463 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
        1366         1058          186         1114           37         1751 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
         738          914         1484         1386          918          571 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
         684          204         1293         1342           67          875 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
         885          655          695          686          260          915 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
         783          847          737          751         1066         1004 
TCGA-36-2532 TCGA-36-2533 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
         897           NA          907          788          763          724 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
         657           68          638          557          624          431 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
         184          492          349          243          792          722 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
         287         1278          227         1240           NA          731 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
         346          643           53          679          882          763 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
         761         5481           NA           NA         3532           NA 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 
          NA           NA          165           NA           NA          338 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
         246          637          956          564          848          132 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
         967          866         1484         1364         1089           74 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
        1024         1329           44          256          176          347 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
         396          276         1038          952         1127         1293 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
        1488         1722         2061         1321          479         1161 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
          61          168          441          547          122          932 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
        1212          932           36         1398         1381          146 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
         145         1573         2182         1875         1776         1844 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
        1993         1688          197         2338          629         1354 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-72-4231 
        3825          676          193          945          262           NA 
TCGA-72-4232 TCGA-72-4233 TCGA-72-4234 TCGA-72-4235 TCGA-72-4236 TCGA-72-4237 
          NA           NA           NA           NA           NA           NA 
TCGA-72-4238 TCGA-72-4240 TCGA-72-4241 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
          NA           NA           NA         1207          576           NA 
TCGA-WR-A838 
         245 
Variable 1:'AGE':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=267,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=452,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'TUMOR.GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'TUMOR.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'PATIENTTUMORRECURRENCESTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'DAYSTOTUMORRECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'CHEMOTHERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 25:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'BATCH.NUMBER':	nDistinctValues=21,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "PRIMARY.SITE.OF.DISEASE"               
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "COMPLETENESS.OF.RESECTION"             
[6] "RACE"                                  
[7] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 571 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=55, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    68  95
  1P GAIN WILD-TYPE 198 195
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              163               393 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               95               195 
$`1P GAIN MUTATED`
TCGA-04-1336 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1364 
       49.15        18.51        11.87        65.52        63.09        33.67 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1649 TCGA-04-1655 TCGA-09-0365 
       38.37       119.08        29.10        64.64        45.37         9.47 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1667 TCGA-09-1670 TCGA-09-2045 
       57.76        35.57         9.99        61.87        17.98        35.15 
TCGA-09-2048 TCGA-09-2051 TCGA-10-0925 TCGA-10-0930 TCGA-13-0717 TCGA-13-0723 
        4.54        63.09        54.31        33.24        24.59        39.58 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0795 
        2.73        31.10        55.17        11.18        11.54        19.59 
TCGA-13-0803 TCGA-13-0885 TCGA-13-0888 TCGA-13-0893 TCGA-13-0897 TCGA-13-0911 
       43.86        91.40        70.39        43.36        57.47        27.72 
TCGA-13-0919 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1495 TCGA-13-1496 
       14.89         6.05         5.92         4.70        49.25         4.24 
TCGA-13-1504 TCGA-13-1506 TCGA-13-1512 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0987 
       16.57         4.41         3.09        10.78         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-23-1031 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       25.94        26.20        18.90        33.30        86.01       129.96 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 
       58.13         0.53        24.95       115.89        91.66        49.84 
TCGA-24-1104 TCGA-24-1417 TCGA-24-1418 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
       63.55         7.82         7.99        19.17        18.67         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       12.46        45.14         9.11         1.18        22.22        26.96 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 
       16.21        56.58        39.88        19.53        44.09        25.87 
TCGA-24-1565 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1924 
       10.26        48.33         8.32         3.48         3.81        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2026 TCGA-24-2029 TCGA-24-2038 TCGA-24-2254 
       11.05        81.11        34.82        14.43        44.52        57.07 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 TCGA-24-2297 TCGA-25-1312 
       31.63        70.45        44.61        36.23        55.86         1.02 
TCGA-25-1313 TCGA-25-1317 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 
       26.96         1.02        33.96        12.00         2.96        15.81 
TCGA-25-1627 TCGA-25-1633 TCGA-25-1635 TCGA-25-2392 TCGA-25-2400 TCGA-29-1698 
        0.36        60.59        51.22         1.02        42.02        68.32 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1764 
       16.90        18.67        41.98        29.23        17.00        62.93 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-1784 
       22.98        24.36        12.36        12.30         7.23         5.36 
TCGA-29-2425 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
       65.00        11.84        38.07        51.91         2.47        15.68 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-31-1959 TCGA-36-1577 TCGA-36-1581 
        6.12        36.62         1.22         2.20        25.74        24.69 
TCGA-36-2529 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-57-1582 TCGA-57-1994 
       35.05        16.18        26.04        23.74        24.03        25.02 
TCGA-59-2351 TCGA-59-2355 TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 TCGA-61-1738 
      116.12         2.14         8.09         4.34        31.79        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1906 TCGA-61-1911 
        2.43        33.67        43.69         8.42        34.13        42.51 
TCGA-61-1914 TCGA-61-1919 TCGA-61-2008 TCGA-61-2009 TCGA-61-2088 TCGA-61-2092 
       56.61        38.17        30.64        39.85         4.77        51.72 
TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2614 
       60.62         6.48        76.87        20.68       125.75         8.61 
TCGA-OY-A56P 
       39.68 

$`1P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1348 
       40.24        41.00         1.81         2.01        46.62        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       21.57        63.98        65.46        49.28        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       76.57        71.47        82.39        56.55        41.59        19.99 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 
       84.20        55.43        48.89        27.88        28.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 TCGA-09-0367 TCGA-09-1661 TCGA-09-1662 
       31.86        47.70        29.16        17.98        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 
       74.93        41.62        57.60        55.36        30.51         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 
        3.02         8.55        97.55         6.18         6.12       112.41 
TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0926 
       71.11        39.75        20.94        26.93        12.46        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       81.47        18.51        32.28        11.70         3.91        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 
       35.80        15.12        19.86         6.21        44.55        12.39 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 
       15.19        17.82         2.50        11.38        34.06        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       30.35         8.71         7.79         8.12         8.28         8.19 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 
       35.28        35.28        13.61        68.94       107.18        74.27 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0899 TCGA-13-0900 
       66.67        61.84        67.99        69.01        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36        47.38        48.33        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 
       37.08        34.06        29.98        21.17        13.81         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 
        6.41         6.08        10.88         6.61         7.36         6.84 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       98.04        20.68        22.39        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       73.55        38.20        54.31        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       32.84         4.21         4.77         4.18         2.56         3.91 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       14.24        12.23         8.61         8.75         6.28        54.77 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       72.20        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.66        47.54        42.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 
       31.76        49.41         8.81        29.13         2.24        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 
       54.51         3.22        31.20        68.68         4.57         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 
        6.38        39.09        33.47        87.48        77.00         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.70         4.50         7.63        19.66        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 
       41.56         7.66        22.32        54.12        47.41         6.31 
TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        6.38         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 
        5.36         4.83        17.39        28.37        43.53        72.92 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 
      105.99         3.45        57.40        64.27        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1562 TCGA-24-1563 
       41.39        58.09        88.50        70.62        45.50        47.70 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1844 TCGA-24-1846 
       17.23        90.15        88.37        38.24         3.72         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 
       11.28         5.79         5.52         9.80        22.68        16.44 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 
        4.87       152.02        44.84        58.16       109.71        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       18.48        28.18        64.01        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 
       47.54         0.82        67.36        16.64        33.11        53.26 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       32.02        51.06        37.02        34.98        65.00        36.95 
TCGA-25-1322 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
        2.99        18.58        18.02        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       56.94        35.54        14.96        24.99        18.05        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       13.02        49.05        38.04         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       19.99         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       44.71        47.18       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 TCGA-29-1762 
       31.20         0.53        59.67        18.25        34.62        85.68 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 
       66.81        39.12        31.23        22.55        17.33        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 
       14.93         8.38        34.62        86.17        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 
        4.90        42.25        11.47         9.76        21.04        36.26 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 TCGA-30-1887 
        0.26        48.10        44.91        34.78        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
        6.71        42.51        44.12        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 
       22.85        22.55         8.55        30.08        27.85        24.23 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       21.60         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
        6.05        11.47         7.99         9.44        42.02         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
       40.77         1.48        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 
       29.00        25.08       180.20        80.12        22.32         9.40 
TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 
       34.39         5.42        44.81        20.52        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       31.43        18.54        27.88        28.47        48.79        44.84 
TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 
        1.45         5.79        11.41        13.02         9.07        31.30 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 
       37.05        48.92        67.76        43.43        15.75         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 
        5.52        14.50        17.98         4.01        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.96        45.40         4.80        71.74        61.64        58.39 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       65.52        55.50        44.52        22.22         6.35        31.07 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         8.05 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.36              0.26 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           129.96            180.20 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            26.04             28.70 
[1] "0.4 - 130.0 (26.0)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1P GAIN MUTATED         1   161                1
  1P GAIN WILD-TYPE       1   396                1
D1V3, multiclass
                  clus
vv                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  OMENTUM                        1                 1
  OVARY                        161               396
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, continuous
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2 165
  1P GAIN WILD-TYPE   1 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2  165
  1P GAIN WILD-TYPE    1  403
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                2                 1
  YES             165               403
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  1P GAIN MUTATED    1  7  2  0
  1P GAIN WILD-TYPE 13 19  3  3
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               1                13
  R1               7                19
  R2               2                 3
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     5
  1P GAIN WILD-TYPE                                3    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P GAIN MUTATED                           8
  1P GAIN WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           0   147
  1P GAIN WILD-TYPE                                         1   328
D1V7, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   5                13
  BLACK OR AFRICAN AMERICAN                               8                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 147               328
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  83
  1P GAIN WILD-TYPE   9 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   83
  1P GAIN WILD-TYPE    9  242
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              83               242
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    94 116
  1Q GAIN WILD-TYPE 172 174
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              210               346 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              116               174 
$`1Q GAIN MUTATED`
TCGA-04-1336 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1356 
       49.15        18.51        11.87        65.52        63.09        49.28 
TCGA-04-1364 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       33.67        56.55        41.59        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-0365 
       84.20        55.43        64.64        31.86        45.37         9.47 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 
       57.76        35.57         9.99        38.43        61.87        55.36 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
       17.98         5.85         8.55         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2051 TCGA-09-2056 TCGA-10-0925 TCGA-10-0930 TCGA-10-0933 
      112.41        63.09        12.46        54.31        33.24        11.70 
TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 
       35.44        19.86        24.59        39.58         2.73        15.19 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0795 TCGA-13-0799 
       55.17        11.18        11.54        32.25        19.59         7.79 
TCGA-13-0800 TCGA-13-0803 TCGA-13-0888 TCGA-13-0890 TCGA-13-0897 TCGA-13-0901 
        8.12        43.86        70.39        67.99        57.47        19.36 
TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       27.72        14.89         4.64         5.92         6.84         4.70 
TCGA-13-1481 TCGA-13-1484 TCGA-13-1495 TCGA-13-1504 TCGA-13-1506 TCGA-13-1512 
       87.06        98.04        49.25        16.57         4.41         3.09 
TCGA-13-2061 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 
       10.78         8.42        23.05        25.94        26.20        25.38 
TCGA-20-1684 TCGA-23-1031 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 TCGA-23-1124 
       19.10        18.90        68.68        86.01       129.96        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 
        0.53        24.95       115.89        22.32        63.55         6.31 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1431 TCGA-24-1436 TCGA-24-1464 
        7.99         0.76         6.25        19.17         8.55        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 
       45.14         9.11         1.18        22.22        26.96        16.21 
TCGA-24-1549 TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 
       56.58        58.09        39.88        19.53        44.09        25.87 
TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 
       10.26        88.37        48.33         8.32         3.48         3.81 
TCGA-24-1924 TCGA-24-1930 TCGA-24-2026 TCGA-24-2029 TCGA-24-2038 TCGA-24-2254 
       30.21        81.11        34.82        14.43        44.52        57.07 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 TCGA-24-2297 TCGA-25-1312 
       31.63        70.45        44.61        36.23        55.86         1.02 
TCGA-25-1313 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       26.96        37.02         1.02        34.98        65.00        36.95 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1633 
       33.96        12.00         2.96        15.81         0.36        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-2392 TCGA-25-2396 TCGA-25-2400 
       35.54        51.22        24.99         1.02         3.02        42.02 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 
       78.90        44.71         0.79        68.32        16.90        18.67 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 
       41.98        29.23        34.62        62.93        39.12        22.98 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-1784 
       24.36        17.33        12.36        12.30         7.23         5.36 
TCGA-29-2425 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       65.00        11.84        11.47        21.04        38.07        51.91 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-31-1959 
        2.47        15.68         6.12        36.62         1.22         2.20 
TCGA-36-1569 TCGA-36-1571 TCGA-36-1576 TCGA-36-1581 TCGA-36-2529 TCGA-36-2551 
       29.10        22.85        30.08        24.69        35.05        16.18 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-57-1582 TCGA-57-1586 TCGA-57-1994 
       11.47        26.04        23.74        24.03        22.32        25.02 
TCGA-59-2351 TCGA-59-2355 TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
      116.12         2.14         8.09         4.34        31.79        28.47 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1904 
       35.80         2.43        33.67        43.69         8.42         9.07 
TCGA-61-1906 TCGA-61-1911 TCGA-61-1914 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 
       34.13        42.51        56.61        38.17         4.01        30.64 
TCGA-61-2009 TCGA-61-2088 TCGA-61-2092 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       39.85         4.77        51.72        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2614 TCGA-OY-A56P 
        6.48        76.87        20.68       125.75         8.61        39.68 

$`1Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1348 
       40.24        41.00         1.81         2.01        46.62        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
       21.57        63.98        65.46        32.52        44.32        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1517 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       71.47        82.39        19.99        48.89        27.88        28.64 
TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 TCGA-09-0367 TCGA-09-1662 TCGA-09-1664 
       36.23        47.70        29.16        17.98        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 
       41.62        57.60        30.51         3.02        97.55         6.18 
TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-10-0926 TCGA-10-0927 
       71.11        39.75        20.94        26.93        25.91        81.47 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 
       18.51        32.28         3.91        35.80        15.12         6.21 
TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 TCGA-13-0758 
       44.55        12.39        31.10        17.82         2.50        11.38 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       34.06        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
       28.70        30.35         8.71         8.28         8.19        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18        91.40        74.27 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 
       66.67        61.84        69.01        43.36        56.15        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       34.06        29.98        21.17        13.81         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 TCGA-13-1412 
       10.88         6.61         7.36         6.05         4.21         5.33 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       54.64        61.71        29.42        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 
       82.88        52.44        73.55        38.20         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1507 
       37.61        38.40        13.97        32.84         4.21         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.91        14.24        12.23         8.61 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 
        8.75         6.28        54.77        72.20        27.52        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
        2.93         2.66        47.54        42.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 
       26.83        31.76        49.41         8.81        29.13         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 
       51.35        54.51         3.22        31.20         4.57        33.30 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2078 TCGA-23-2079 
        4.27         6.38        39.09        33.47        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
       19.66        11.64        21.80        41.56         7.66        54.12 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1424 TCGA-24-1425 
       47.41         6.38         7.82         7.86         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        17.39        28.37        18.67        43.53 
TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 
       72.92       105.99         3.45        57.40        64.27        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1562 TCGA-24-1563 
       51.91        41.39        88.50        70.62        45.50        47.70 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 
       17.23        90.15        38.24         3.72         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 
        5.79         5.52         9.80        22.68        16.44        11.05 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 
        4.87       152.02        44.84        58.16       109.71        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       18.48        28.18        64.01        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 
       47.54         0.82        67.36        16.64        33.11        53.26 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1322 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 
       32.02        51.06         2.99        18.58        18.02        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 
        7.86         0.30        56.94        14.96        18.05        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       13.02        49.05        38.04        12.00        45.01        19.99 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1691 TCGA-29-1693 
        2.96        29.03        31.00        26.99        47.18       101.79 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 
       38.53        33.70        31.20         0.53        59.67        18.25 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1768 TCGA-29-1771 TCGA-29-1776 
       17.00        85.68        66.81        31.23        22.55        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 
       14.93         8.38        34.62        86.17        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 
        4.90        42.25         9.76        36.26         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       44.91        34.78        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 
       44.12        28.77        21.53        22.55         8.55        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       27.85        24.23        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2588 TCGA-42-2589 
       20.52        14.17         6.05         7.99         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
        7.46        40.77         1.48        11.38        21.14         1.74 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 
       29.00        25.08       180.20        80.12        22.32         9.40 
TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 
       34.39         5.42        44.81        20.52        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1736 TCGA-61-1737 TCGA-61-1895 
       31.43        18.54        27.88        48.79        44.84         1.45 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 
        5.79        11.41        13.02        31.30        37.05        48.92 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       67.76        43.43        15.75         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       17.98        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 
       71.74        61.64        58.39        44.52        22.22         6.35 
TCGA-61-2613 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07        18.94         0.79         8.05 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.36              0.26 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           129.96            180.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            26.58             28.67 
[1] "0.4 - 130.0 (26.6)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1Q GAIN MUTATED         1   208                2
  1Q GAIN WILD-TYPE       1   349                0
D2V3, multiclass
                  clus
vv                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  OMENTUM                        1                 1
  OVARY                        208               349
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, continuous
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     1 217
  1Q GAIN WILD-TYPE   2 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1  217
  1Q GAIN WILD-TYPE    2  351
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                1                 2
  YES             217               351
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED    4  7  2  0
  1Q GAIN WILD-TYPE 10 19  3  3
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0               4                10
  R1               7                19
  R2               2                 3
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     6
  1Q GAIN WILD-TYPE                                3    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q GAIN MUTATED                          10
  1Q GAIN WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           0   188
  1Q GAIN WILD-TYPE                                         1   287
D2V7, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   6                12
  BLACK OR AFRICAN AMERICAN                              10                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 188               287
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     4 111
  1Q GAIN WILD-TYPE   6 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4  111
  1Q GAIN WILD-TYPE    6  214
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 6
  NOT HISPANIC OR LATINO             111               214
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    84  93
  2P GAIN WILD-TYPE 182 197
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              177               379 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               93               197 
$`2P GAIN MUTATED`
TCGA-04-1336 TCGA-04-1342 TCGA-04-1347 TCGA-04-1350 TCGA-04-1356 TCGA-04-1364 
       49.15        18.51        63.09        63.98        49.28        33.67 
TCGA-04-1371 TCGA-04-1525 TCGA-04-1542 TCGA-04-1646 TCGA-04-1655 TCGA-09-0364 
       82.39        38.37        84.20        27.88        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1661 TCGA-09-1670 TCGA-09-1672 
        9.47        57.76        35.57        38.43        17.98         5.85 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 TCGA-10-0927 TCGA-10-0933 TCGA-10-0935 
        8.55         6.18         4.54        81.47        11.70        35.44 
TCGA-10-0938 TCGA-13-0724 TCGA-13-0730 TCGA-13-0757 TCGA-13-0760 TCGA-13-0800 
       19.86         2.73        17.82        11.18        11.54         8.12 
TCGA-13-0802 TCGA-13-0884 TCGA-13-0888 TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 
        8.19       107.18        70.39        43.36        56.15        19.36 
TCGA-13-0906 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-1407 TCGA-13-1409 
       44.94        14.89        13.81         4.64         6.05         6.84 
TCGA-13-1410 TCGA-13-1412 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-2057 
        4.70         5.33        32.84        16.57         4.21        14.24 
TCGA-13-2060 TCGA-13-A5FU TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 
        8.61         8.42         2.93         2.66        47.54        15.39 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 
       68.68        86.01       129.96         6.38        39.09         0.53 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2643 TCGA-24-0970 TCGA-24-0982 TCGA-24-1417 
       24.95        87.48         4.70        11.64        22.32         7.82 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 TCGA-24-1434 TCGA-24-1436 TCGA-24-1467 
        7.99         0.76         6.02        18.67         8.55       105.99 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1552 TCGA-24-1553 
        9.11         1.18        22.22        26.96        41.39        58.09 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 
       19.53        44.09        88.37        38.24         8.32         3.72 
TCGA-24-1845 TCGA-24-1850 TCGA-24-1924 TCGA-24-1928 TCGA-24-2019 TCGA-24-2029 
        3.81         5.52        30.21        11.05         4.87        14.43 
TCGA-24-2033 TCGA-24-2261 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 
       18.48         0.79        44.61         0.82        67.36        33.11 
TCGA-25-1312 TCGA-25-1315 TCGA-25-1317 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 
        1.02        51.06         1.02        65.00         2.96        18.58 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 
       15.81        20.61         0.30        35.54        14.96        18.05 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2398 TCGA-25-2400 TCGA-25-2409 TCGA-29-1691 
       49.05        38.04        45.01        42.02        26.99        47.18 
TCGA-29-1695 TCGA-29-1701 TCGA-29-1702 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 
        0.79        16.90        18.67        66.81        62.93        22.98 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-2425 TCGA-29-2429 TCGA-29-A5NZ 
       17.33        12.36        14.93        65.00         4.90        21.04 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1859 TCGA-30-1862 TCGA-31-1950 TCGA-31-1953 
       38.07        51.91        48.10         6.12        18.77         6.71 
TCGA-31-1959 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 
        2.20        22.85         8.55        30.08        27.85        24.69 
TCGA-36-2547 TCGA-36-2552 TCGA-42-2587 TCGA-42-2589 TCGA-57-1582 TCGA-57-1583 
       20.52        11.47        23.74        42.02        24.03        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2352 TCGA-59-2372 
        1.74        22.32        25.02       180.20         9.40        44.81 
TCGA-59-A5PD TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1741 
       20.52         8.09        27.88         4.34        31.79        33.67 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1906 TCGA-61-1919 TCGA-61-2000 TCGA-61-2003 
        8.42         5.79        34.13        38.17        14.50         4.01 
TCGA-61-2009 TCGA-61-2018 TCGA-61-2088 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       39.85        45.40         4.77        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 
        6.48        76.87       125.75        22.22         6.35         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
       39.68        18.94         8.05 

$`2P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       40.24        41.00         1.81         2.01        46.62        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 
       65.52        48.76        21.57        65.46        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 
       76.57        71.47        56.55        41.59        19.99       119.08 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       29.10        55.43        48.89        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-09-0367 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 
       31.86        47.70        17.98         9.99        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 
       41.62        57.60        61.87        55.36        30.51         3.02 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
       97.55         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       39.75        20.94        26.93        12.46        54.31        25.91 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 
       18.51        33.24        32.28         3.91        35.80        15.12 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 
        6.21        24.59        44.55        39.58        12.39        31.10 
TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 
       15.19        55.17         2.50        11.38        34.06        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 
       30.35        19.59         8.71         7.79         8.28        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 
       35.28        35.28        13.61        68.94        91.40        74.27 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0900 
       66.67        61.84        67.99        69.01        57.47        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        47.84        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       34.06        29.98        21.17         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 
        6.61         7.36         5.92         4.21        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       61.71        29.42        98.04        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1506 TCGA-13-1507 
       54.31        37.61        38.40        13.97         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 
        4.18         2.56         3.91         3.09        12.23        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        8.75         6.28        54.77        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1022 
       72.20        27.52        25.38        19.10        16.70        42.54 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       18.90         2.24        51.35        54.51         3.22        31.20 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 
        4.57        33.30         4.27        33.47        58.13       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 
       91.66        77.00        49.84         2.76         4.50         7.63 
TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
       19.66        21.80        41.56         7.66        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 
       47.41         6.31         6.38         7.86         6.25         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        5.36         4.83        17.39        28.37        19.17        43.53 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 
       72.92        12.46        45.14         3.45        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1556 
       16.21        56.58        41.06        51.91        88.50        70.62 
TCGA-24-1557 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       39.88        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
       90.15        48.33         3.48         4.37        11.28         5.79 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 
        9.80        22.68        16.44        81.11       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       58.16        34.82       109.71        53.95        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       44.52        57.07        36.16         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 
       70.45        36.23        16.64        55.86        53.26        26.96 
TCGA-25-1314 TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       32.02        37.02        34.98        36.95        33.96         2.99 
TCGA-25-1323 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 
       12.00        18.02         0.36         7.86        56.94        60.59 
TCGA-25-1635 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2396 
       51.22        24.99        85.05        13.02         1.02         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 
       12.00        19.99         2.96        29.03        31.00        78.90 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
       44.71       101.79        38.53        33.70        31.20        68.32 
TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
        0.53        59.67        18.25        41.98        29.23        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 
       17.00        85.68        39.12        31.23        24.36        22.55 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       11.84        12.30         8.38         7.23         5.36        34.62 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       86.17        62.47        45.11        42.25        11.84        11.47 
TCGA-29-2436 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 
        9.76        36.26         2.47        15.68         0.26        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
       34.78        36.62         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 
       48.79        45.57        30.18        22.49        42.51        44.12 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1580 
       28.77        29.10        21.53        22.55        25.74        24.23 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 
       23.80        21.60         2.24        20.98        18.31        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 
        6.05        16.18         7.99        26.04         9.44         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-59-2349 
       40.77         1.48        21.14        29.00        25.08        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 
       22.32       116.12        34.39         2.14         5.42        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       20.94        31.43        18.54        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1901 TCGA-61-1903 
       35.80         2.43        43.69         1.45        11.41        13.02 
TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
        9.07        31.30        37.05        42.51        48.92        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 
       67.76        43.43        15.75         2.01         5.52        17.98 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 
       30.64        30.64         1.18        45.96         4.80        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2109 TCGA-61-2110 TCGA-61-2613 
       71.74        61.64        58.39        20.68        44.52        31.07 
TCGA-VG-A8LO 
        0.79 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.30              0.26 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           180.20            152.02 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            19.53             30.64 
[1] "0.3 - 180.2 (19.5)" "0.3 - 152.0 (30.6)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  2P GAIN MUTATED         0   178                0
  2P GAIN WILD-TYPE       2   379                2
D3V3, multiclass
                  clus
vv                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                        178               379
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, continuous
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1 182
  2P GAIN WILD-TYPE   2 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1  182
  2P GAIN WILD-TYPE    2  386
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                1                 2
  YES             182               386
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED    4  6  2  1
  2P GAIN WILD-TYPE 10 20  3  2
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               4                10
  R1               6                20
  R2               2                 3
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     4
  2P GAIN WILD-TYPE                                3    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P GAIN MUTATED                          12
  2P GAIN WILD-TYPE                        20
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           0   154
  2P GAIN WILD-TYPE                                         1   321
D3V7, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   4                14
  BLACK OR AFRICAN AMERICAN                              12                20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 154               321
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     3  96
  2P GAIN WILD-TYPE   7 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3   96
  2P GAIN WILD-TYPE    7  229
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO              96               229
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    66  82
  2Q GAIN WILD-TYPE 200 208
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              148               408 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               82               208 
$`2Q GAIN MUTATED`
TCGA-04-1347 TCGA-04-1350 TCGA-04-1356 TCGA-04-1364 TCGA-04-1516 TCGA-04-1536 
       63.09        63.98        49.28        33.67        41.59        29.10 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1655 TCGA-09-0365 TCGA-09-0366 
       84.20        27.88        64.64        45.37         9.47        57.76 
TCGA-09-0369 TCGA-09-1661 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       35.57        38.43        17.98         5.85         8.55         6.18 
TCGA-09-2048 TCGA-10-0927 TCGA-10-0933 TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 
        4.54        81.47        11.70        35.44        19.86         2.73 
TCGA-13-0730 TCGA-13-0757 TCGA-13-0760 TCGA-13-0800 TCGA-13-0883 TCGA-13-0884 
       17.82        11.18        11.54         8.12        68.94       107.18 
TCGA-13-0888 TCGA-13-0893 TCGA-13-0901 TCGA-13-0906 TCGA-13-0919 TCGA-13-0920 
       70.39        43.36        19.36        44.94        14.89        13.81 
TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1488 TCGA-13-1496 
        6.05         6.84         4.70         5.33        70.82         4.24 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-2057 TCGA-13-2060 TCGA-20-1687 
       32.84        16.57         4.21        14.24         8.61         2.66 
TCGA-23-1021 TCGA-23-1024 TCGA-23-1111 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 
       47.54        15.39         3.22        68.68        86.01       129.96 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2072 TCGA-23-2643 TCGA-24-0982 
        6.38        39.09         0.53        24.95         4.70        22.32 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 TCGA-24-1430 TCGA-24-1434 TCGA-24-1436 
        7.99         0.76         6.02        28.37        18.67         8.55 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1553 
      105.99         9.11         1.18        22.22        26.96        58.09 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 
       19.53        44.09        88.37        38.24         8.32         3.72 
TCGA-24-1850 TCGA-24-1924 TCGA-24-1928 TCGA-24-2033 TCGA-24-2261 TCGA-24-2288 
        5.52        30.21        11.05        18.48         0.79         0.82 
TCGA-24-2289 TCGA-24-2295 TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1329 
       67.36        33.11         1.02        65.00        33.96         2.96 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 
       18.58        15.81        35.54        14.96        18.05        85.05 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1696 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 
       47.18         0.79        33.70        66.81        62.93        22.98 
TCGA-29-1775 TCGA-29-1778 TCGA-29-2425 TCGA-29-2429 TCGA-30-1714 TCGA-30-1718 
       12.36        14.93        65.00         4.90        38.07        51.91 
TCGA-30-1859 TCGA-30-1862 TCGA-31-1950 TCGA-31-1959 TCGA-36-1576 TCGA-36-1578 
       48.10         6.12        18.77         2.20        30.08        27.85 
TCGA-36-1581 TCGA-36-2547 TCGA-36-2552 TCGA-42-2587 TCGA-57-1582 TCGA-57-1583 
       24.69        20.52        11.47        23.74        24.03        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2352 TCGA-59-A5PD 
        1.74        22.32        25.02       180.20         9.40        20.52 
TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 
        8.09         4.34        31.79        33.67        43.69         8.42 
TCGA-61-1906 TCGA-61-1919 TCGA-61-2003 TCGA-61-2012 TCGA-61-2018 TCGA-61-2088 
       34.13        38.17         4.01        30.64        45.40         4.77 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2113 
       60.62        65.52        55.50         6.48        76.87        22.22 
TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
        6.35         8.61        39.68        18.94 

$`2Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 
       18.51        11.87        65.52        48.76        21.57        65.46 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       32.52        44.32        76.57        71.47        82.39        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       19.99        38.37       119.08        55.43        48.89        28.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 TCGA-09-0367 TCGA-09-1659 
       36.23        31.86        47.70        29.16        17.98         9.99 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       89.33        74.93        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 
       30.51         3.02        97.55         6.12        35.15       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 
       54.31        25.91        18.51        33.24        32.28         3.91 
TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       35.80        15.12         6.21        24.59        44.55        39.58 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 
       12.39        31.10        15.19        55.17         2.50        11.38 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       34.06        32.25        31.04        21.40         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       36.72        28.70        30.35        19.59         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        43.86        35.28        35.28        13.61 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       91.40        74.27        66.67        61.84        67.99        69.01 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       57.47        56.15        57.07        47.38        48.33        47.84 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1408 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        5.92         4.21        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       98.04        20.68        22.39        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       38.20        49.25        54.31        37.61        38.40        13.97 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.41         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
       12.23        10.78         8.75         6.28        54.77         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       23.05        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
       19.10        16.70         2.93        42.54        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       31.76        49.41         8.81        29.13        18.90         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 
       51.35        54.51        31.20         4.57        33.30         4.27 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       33.47        58.13       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
       49.84         2.76         4.50         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       21.80        41.56         7.66        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 
        6.31         6.38         7.82         7.86         6.25         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 
        5.36         4.83        17.39        19.17        43.53        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
       12.46        45.14         3.45        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 
       56.58        41.06        51.91        41.39        88.50        70.62 
TCGA-24-1557 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       39.88        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       90.15        48.33         3.48         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 
        5.79         9.80        22.68        16.44        81.11         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
      152.02        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       53.95        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 
        0.36        47.54        31.63        70.45        44.61        36.23 
TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       16.64        55.86        53.26         1.02        26.96        32.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
       51.06        37.02        34.98        36.95         2.99        12.00 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       18.02         0.36        20.61         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       60.59        51.22        24.99        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       38.04         3.02        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        44.71 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
      101.79        38.53        31.20        68.32         0.53        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       18.67        59.67        18.25        41.98        29.23        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 
       17.00        85.68        39.12        31.23        24.36        22.55 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       17.33        11.84        12.30         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 
       34.62        86.17        62.47        45.11        42.25        11.84 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       11.47         9.76        21.04        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
        0.26        44.91        34.78        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 
       24.26        30.05        48.79        45.57        30.18        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
        6.71        42.51        44.12        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-2529 
       22.85        22.55         8.55        25.74        24.23        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 
       21.60         2.24        20.98        18.31        14.17         6.05 
TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       16.18         7.99        26.04         9.44        42.02         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-59-2349 
       40.77         1.48        21.14        29.00        25.08        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       22.32       116.12        34.39         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 
       11.11        20.94        31.43        18.54        27.88        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1900 
       48.79        44.84        35.80         2.43         1.45         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       11.41        13.02         9.07        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 
       48.92        56.61        67.76        43.43        15.75         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 
        5.52        14.50        17.98        30.64        39.85         1.18 
TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.96         4.80        51.72        71.74        61.64        58.39 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 
       20.68        44.52       125.75        31.07         0.79         8.05 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.53              0.26 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           180.20            152.02 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           21.370            29.655 
[1] "0.5 - 180.2 (21.4)" "0.3 - 152.0 (29.7)"
[1] "hr=" "1.2"
D4V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  2Q GAIN MUTATED         0   148                0
  2Q GAIN WILD-TYPE       2   409                2
D4V3, multiclass
                  clus
vv                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                        148               409
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, continuous
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2 150
  2Q GAIN WILD-TYPE   1 418
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2  150
  2Q GAIN WILD-TYPE    1  418
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                2                 1
  YES             150               418
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  2Q GAIN MUTATED    3  6  1  1
  2Q GAIN WILD-TYPE 11 20  4  2
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0               3                11
  R1               6                20
  R2               1                 4
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     2
  2Q GAIN WILD-TYPE                                3    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q GAIN MUTATED                          10
  2Q GAIN WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           0   131
  2Q GAIN WILD-TYPE                                         1   344
D4V7, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                              10                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 131               344
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     3  77
  2Q GAIN WILD-TYPE   7 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   77
  2Q GAIN WILD-TYPE    7  248
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO              77               248
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    73  82
  3P GAIN WILD-TYPE 193 208
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              155               401 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               82               208 
$`3P GAIN MUTATED`
TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1349 TCGA-04-1371 
       41.00         2.01        46.62        11.87        21.57        82.39 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1646 TCGA-04-1655 TCGA-09-0364 
       41.59        19.99        29.10        27.88        45.37        29.16 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1665 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
       17.98         9.99        41.62        55.36        17.98         5.85 
TCGA-09-1674 TCGA-09-2043 TCGA-10-0930 TCGA-10-0935 TCGA-10-0936 TCGA-13-0723 
        8.55         6.18        33.24        35.44        35.80        39.58 
TCGA-13-0724 TCGA-13-0751 TCGA-13-0760 TCGA-13-0762 TCGA-13-0795 TCGA-13-0800 
        2.73        55.17        11.54        32.25        19.59         8.12 
TCGA-13-0803 TCGA-13-0884 TCGA-13-0911 TCGA-13-0921 TCGA-13-1403 TCGA-13-1410 
       43.86       107.18        27.72         4.64        10.88         4.70 
TCGA-13-1484 TCGA-13-1489 TCGA-13-1495 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 
       98.04        82.88        49.25        16.57         4.21         4.77 
TCGA-13-2061 TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 
       10.78        26.20        25.38        19.10         2.93         2.66 
TCGA-23-1026 TCGA-23-1109 TCGA-23-1110 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 
       26.83        51.35        54.51         4.57        33.30       129.96 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2643 TCGA-24-0979 
       24.95       115.89        87.48        91.66         4.70        41.56 
TCGA-24-0982 TCGA-24-1413 TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 TCGA-24-1434 
       22.32         6.31         6.02         5.36        17.39        18.67 
TCGA-24-1436 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1553 
        8.55       105.99         3.45         1.18        22.22        58.09 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1564 TCGA-24-1567 TCGA-24-1614 TCGA-24-1842 
       39.88        19.53        25.87        17.23        48.33         8.32 
TCGA-24-1844 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
        3.72        11.28         5.52         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2038 TCGA-24-2261 
       16.44        11.05         4.87       152.02        44.52         0.79 
TCGA-24-2267 TCGA-24-2295 TCGA-24-2298 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 
       47.54        33.11        53.26        34.98        65.00        33.96 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1634 TCGA-25-1635 TCGA-25-1877 
        2.96        18.58        15.81        35.54        51.22        18.05 
TCGA-25-1878 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-29-1694 TCGA-29-1698 
       85.05        45.01        42.02        29.03        38.53        68.32 
TCGA-29-1701 TCGA-29-1705 TCGA-29-1710 TCGA-29-1761 TCGA-29-1770 TCGA-29-1778 
       16.90        18.25        29.23        17.00        24.36        14.93 
TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-30-1718 
        7.23        86.17        65.00        45.11        42.25        51.91 
TCGA-30-1859 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1892 TCGA-31-1950 
       48.10        34.78        36.62         1.22        48.79        18.77 
TCGA-36-1578 TCGA-36-2529 TCGA-36-2543 TCGA-42-2587 TCGA-42-2590 TCGA-57-1582 
       27.85        35.05         2.24        23.74         7.46        24.03 
TCGA-57-1585 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-A5PD TCGA-61-1899 
        1.74        25.02       116.12         9.40        20.52         8.42 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1915 
       11.41        13.02         9.07        34.13        31.30        67.76 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2097 TCGA-61-2102 
       17.98         4.01        30.64        39.85        60.62         6.48 
TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75         6.35         8.61        39.68        18.94 

$`3P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 
       40.24         1.81        49.15        18.51        65.52        63.09 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       48.76        63.98        65.46        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1525 TCGA-04-1530 
       33.67        76.57        71.47        56.55        38.37       119.08 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       84.20        55.43        48.89        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1661 
       31.86        47.70         9.47        57.76        35.57        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1673 
       89.33        74.93        57.60        61.87        30.51         3.02 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
       97.55         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       63.09        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       25.91        81.47        18.51        32.28        11.70         3.91 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 
       15.12        19.86         6.21        24.59        44.55        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       31.10        15.19        17.82         2.50        11.18        11.38 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       34.06        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 
       28.70        30.35         8.71         7.79         8.28         8.19 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 
       35.28        35.28        13.61        68.94        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       66.67        70.39        61.84        67.99        69.01        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       57.47        56.15        57.07        19.36        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 
       47.84        44.94        44.84        37.08        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1404 
       21.17        14.89        13.81         6.41         6.08         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 
        7.36         6.05         5.92         6.84         4.21         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 
       54.64        87.06        61.71        29.42        20.68        22.39 
TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 
       70.82        52.44        73.55        38.20         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1506 TCGA-13-1509 
       37.61        38.40        13.97        32.84         4.41         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        2.56         3.91         3.09        14.24        12.23         8.61 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.75         6.28        54.77         8.42        23.05        25.94 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       72.20        27.52        16.70        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       15.39        31.76        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 TCGA-23-1120 
        2.24         3.22        31.20        68.68        86.01         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2081 
        6.38        39.09        33.47        58.13         0.53        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
       49.84         2.76         4.50         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 
       21.80         7.66        54.12        63.55        47.41         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 
        7.82         7.99         7.86         0.76         6.25         5.95 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 
        4.83        28.37        19.17        43.53        72.92        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
       45.14         9.11        26.96        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 
       56.58        41.06        51.91        41.39        88.50        70.62 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 
       44.09        45.50        47.70        10.26        90.15        88.37 
TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1930 
       38.24         3.48         3.81         4.37         5.79        81.11 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 
       18.48        28.18        64.01        57.07        36.16         0.36 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       31.63        70.45        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       16.64        55.86         1.02        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 
       37.02         1.02        36.95         2.99        12.00        18.02 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
        0.36        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       14.96        24.99        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 
        3.02        12.00        19.99         2.96        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1696 
       78.90        44.71        47.18       101.79         0.79        33.70 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1711 
       31.20         0.53        18.67        59.67        41.98        34.62 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
       85.68        66.81        62.93        39.12        31.23        22.98 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       22.55        17.33        12.36        11.84        12.30         8.38 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 
        5.36        34.62        62.47         4.90        11.84        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
        9.76        21.04        38.07        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1862 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
        0.26        44.91         6.12        57.57        24.26        30.05 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       45.57        30.18        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 
        8.55        30.08        25.74        24.23        24.69        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       20.98        18.31        20.52        14.17         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 
       11.47         7.99        26.04         9.44        42.02        40.77 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
        1.48        11.38        21.14        22.32        29.00        25.08 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
      180.20        80.12        22.32        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       44.81        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 
       35.80         2.43        33.67        43.69         1.45         5.79 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 
       37.05        42.51        48.92        56.61        43.43        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2012 TCGA-61-2016 
       38.17         2.01         5.52        14.50        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 
       61.64        58.39        65.52        55.50        76.87        20.68 
TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 
       44.52        22.22        31.07         0.79         8.05 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.79              0.26 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           152.02            180.20 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            24.95             29.13 
[1] "0.8 - 152.0 (24.9)" "0.3 - 180.2 (29.1)"
[1] "hr=" "1"  
D5V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3P GAIN MUTATED         0   156                1
  3P GAIN WILD-TYPE       2   401                1
D5V3, multiclass
                  clus
vv                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                        156               401
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, continuous
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0 160
  3P GAIN WILD-TYPE   3 408
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0  160
  3P GAIN WILD-TYPE    3  408
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                 3
  YES             160               408
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  3P GAIN MUTATED    2 10  1  1
  3P GAIN WILD-TYPE 12 16  4  2
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               2                12
  R1              10                16
  R2               1                 4
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  1     3
  3P GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED                           7
  3P GAIN WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           1   140
  3P GAIN WILD-TYPE                                         0   335
D5V7, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   3                15
  BLACK OR AFRICAN AMERICAN                               7                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 140               335
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  85
  3P GAIN WILD-TYPE   8 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   85
  3P GAIN WILD-TYPE    8  240
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              85               240
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   127 138
  3Q GAIN WILD-TYPE 139 152
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              265               291 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              138               152 
$`3Q GAIN MUTATED`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       41.00         1.81        49.15         2.01        46.62        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 
       65.52        63.09        21.57        63.98        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       33.67        76.57        82.39        41.59        19.99        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1655 TCGA-09-0364 
      119.08        29.10        84.20        27.88        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1665 
        9.47        57.76        17.98        35.57         9.99        41.62 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       55.36        30.51        17.98         5.85         8.55         6.18 
TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 TCGA-10-0930 TCGA-10-0933 
        6.12         4.54       112.41        39.75        33.24        11.70 
TCGA-10-0935 TCGA-10-0936 TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 TCGA-13-0751 
       35.44        35.80        39.58         2.73        15.19        55.17 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0768 TCGA-13-0795 TCGA-13-0800 TCGA-13-0802 
       11.18        11.54         8.45        19.59         8.12         8.19 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0884 TCGA-13-0888 TCGA-13-0897 TCGA-13-0901 
       43.86        35.28       107.18        70.39        57.47        19.36 
TCGA-13-0911 TCGA-13-0920 TCGA-13-0921 TCGA-13-1403 TCGA-13-1409 TCGA-13-1410 
       27.72        13.81         4.64        10.88         6.84         4.70 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1495 
        4.21        87.06        98.04        22.39        82.88        49.25 
TCGA-13-1496 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-2057 
        4.24        16.57         4.21         4.41         4.77        14.24 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
        8.61        10.78         8.75         8.42        25.94        26.20 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1026 
       25.38        19.10         2.93         2.66        47.54        26.83 
TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 
        8.81        18.90        51.35        54.51        68.68         4.57 
TCGA-23-1117 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 
       33.30       129.96        39.09        33.47         0.53        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2084 TCGA-23-2643 TCGA-24-0970 
      115.89        87.48        91.66        49.84         4.70        11.64 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1413 TCGA-24-1417 TCGA-24-1424 TCGA-24-1426 
       41.56        22.32         6.31         7.82         6.02         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 TCGA-24-1467 TCGA-24-1470 
        4.83        17.39        18.67         8.55       105.99         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1548 TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 
        1.18        22.22        16.21        58.09        39.88        19.53 
TCGA-24-1564 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       25.87        17.23        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        3.48         3.72        11.28         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       30.21        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2026 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
       34.82        18.48        44.52        36.16         0.79        47.54 
TCGA-24-2280 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1317 TCGA-25-1318 
       70.45        33.11        53.26         1.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       65.00        33.96        12.00         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       15.81         0.36         7.86        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 
       24.99        18.05        85.05         3.02        45.01        42.02 
TCGA-25-2404 TCGA-29-1693 TCGA-29-1694 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 
       29.03       101.79        38.53        68.32        16.90        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1761 TCGA-29-1764 TCGA-29-1766 
       59.67        18.25        29.23        17.00        62.93        39.12 
TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1783 TCGA-29-2414 
       24.36        12.36        11.84        14.93         7.23        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ 
       65.00        45.11        42.25        11.84        11.47        21.04 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 TCGA-30-1866 
       51.91        36.26         0.26        48.10        34.78        36.62 
TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1950 TCGA-31-1956 TCGA-36-1569 
        1.22        24.26        48.79        18.77        44.12        29.10 
TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       22.55        30.08        27.85        24.69        35.05        33.01 
TCGA-36-2534 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 
       29.82         2.24        18.31        20.52        14.17        16.18 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 
       11.47        23.74         7.46         1.48        24.03         1.74 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       22.32        25.08        25.02        22.32       116.12         9.40 
TCGA-59-A5PD TCGA-61-1722 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1899 
       20.52         8.09        18.54        27.88        31.79         8.42 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1914 
       11.41        13.02         9.07        34.13        31.30        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2002 TCGA-61-2003 
       67.76        43.43        15.75        38.17        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 
       30.64        39.85        60.62        65.52         6.48        76.87 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75        22.22         6.35         8.61        39.68        18.94 
TCGA-VG-A8LO 
        0.79 

$`3Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1342 TCGA-04-1348 TCGA-04-1351 TCGA-04-1356 TCGA-04-1367 
       40.24        18.51        48.76        65.46        49.28        71.47 
TCGA-04-1514 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       56.55        55.43        48.89        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       31.86        47.70        38.43        89.33        74.93        57.60 
TCGA-09-1667 TCGA-09-1673 TCGA-09-1675 TCGA-09-2045 TCGA-09-2050 TCGA-09-2051 
       61.87         3.02        97.55        35.15        71.11        63.09 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        54.31        25.91        81.47 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       18.51        32.28         3.91        15.12        19.86         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 
       24.59        44.55        12.39        31.10        17.82         2.50 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 
       11.38        34.06        32.25        31.04        21.40        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       36.72        28.70        30.35         8.71         7.79         8.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       35.28        13.61        68.94        91.40        74.27        66.67 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 
       61.84        67.99        69.01        43.36        56.15        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-0924 
       34.06        29.98        21.17        14.89         6.41         6.08 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1412 TCGA-13-1477 
        6.61         7.36         6.05         5.92         5.33        54.64 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       61.71        29.42        20.68        70.82        52.44        73.55 
TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       38.20        54.31        37.61        38.40        13.97        32.84 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2071 
        4.18         2.56         3.91         3.09        12.23         6.28 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 TCGA-23-1022 
       54.77        23.05        72.20        27.52        16.70        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1032 
       40.54        15.39        31.76        49.41        29.13         2.24 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 
        3.22        31.20        86.01         4.27         6.38        58.13 
TCGA-23-2081 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0975 
       77.00         2.76         4.50         7.63        19.66        21.80 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1418 
        7.66        54.12        63.55        47.41         6.38         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1430 TCGA-24-1431 
        7.86         0.76         6.25         5.95        28.37        19.17 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1544 
       43.53        72.92        12.46        45.14         9.11        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        56.58        41.06        51.91        41.39 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 
       88.50        70.62        44.09        45.50        47.70        10.26 
TCGA-24-1603 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-2023 TCGA-24-2024 
       90.15         3.81         4.37         5.79        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 
      109.71        14.43        53.95        28.18        64.01        57.07 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
        0.36        31.63        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2297 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       16.64        55.86        26.96        32.02        51.06        37.02 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       36.95         2.99        20.61         0.30        56.94        60.59 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2399 
       13.02        49.05         1.02        38.04        12.00        19.99 
TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
        2.96        31.00        26.99        78.90        44.71        47.18 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1707 TCGA-29-1711 
        0.79        33.70        31.20         0.53        41.98        34.62 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 
       85.68        66.81        31.23        22.98        22.55        17.33 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 
       12.30         8.38         5.36        34.62        62.47         4.90 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 TCGA-30-1860 TCGA-30-1862 
        9.76        38.07         2.47        15.68        44.91         6.12 
TCGA-30-1880 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
       57.57        30.05        45.57        30.18        22.49         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 
       42.51         2.20        28.77        21.53        22.85         8.55 
TCGA-36-1577 TCGA-36-1580 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       25.74        24.23        29.49        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 
       21.60        20.98         6.05         7.99        26.04         9.44 
TCGA-42-2589 TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-57-1992 TCGA-59-2348 
       42.02        40.77        11.38        21.14        29.00       180.20 
TCGA-59-2349 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 
       80.12        34.39         2.14         5.42        44.81        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       20.94        31.43         4.34        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 
       35.80         2.43        33.67        43.69         1.45         5.79 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       37.05        42.51        48.92         2.01         5.52        14.50 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 TCGA-61-2109 
       51.72        71.74        61.64        58.39        55.50        20.68 
TCGA-61-2110 TCGA-61-2613 TCGA-WR-A838 
       44.52        31.07         8.05 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.26              0.30 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           152.02            180.20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            23.74             31.07 
[1] "0.3 - 152.0 (23.7)" "0.3 - 180.2 (31.1)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3Q GAIN MUTATED         0   266                2
  3Q GAIN WILD-TYPE       2   291                0
D6V3, multiclass
                  clus
vv                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                        266               291
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, continuous
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     0 271
  3Q GAIN WILD-TYPE   3 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0  271
  3Q GAIN WILD-TYPE    3  297
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                0                 3
  YES             271               297
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED    7 16  4  1
  3Q GAIN WILD-TYPE  7 10  1  2
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0               7                 7
  R1              16                10
  R2               4                 1
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  2     8
  3Q GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED                          13
  3Q GAIN WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           1   229
  3Q GAIN WILD-TYPE                                         0   246
D6V7, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 1
  ASIAN                                                   8                10
  BLACK OR AFRICAN AMERICAN                              13                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 229               246
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     3 147
  3Q GAIN WILD-TYPE   7 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3  147
  3Q GAIN WILD-TYPE    7  178
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             147               178
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    24  34
  4P GAIN WILD-TYPE 242 256
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               58               498 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               34               256 
$`4P GAIN MUTATED`
TCGA-04-1349 TCGA-04-1356 TCGA-04-1364 TCGA-04-1525 TCGA-04-1530 TCGA-04-1646 
       21.57        49.28        33.67        38.37       119.08        27.88 
TCGA-09-1668 TCGA-09-2048 TCGA-10-0926 TCGA-13-0714 TCGA-13-0794 TCGA-13-0802 
       55.36         4.54        25.91         6.21        30.35         8.19 
TCGA-13-0883 TCGA-13-0920 TCGA-13-1483 TCGA-13-1499 TCGA-13-1505 TCGA-13-2060 
       68.94        13.81        29.42        38.40         4.21         8.61 
TCGA-13-A5FU TCGA-23-1026 TCGA-23-1110 TCGA-23-1114 TCGA-23-2645 TCGA-24-1427 
        8.42        26.83        54.51        68.68         4.50         4.83 
TCGA-24-1428 TCGA-24-1464 TCGA-24-1545 TCGA-24-1558 TCGA-24-1843 TCGA-24-1928 
       17.39        12.46        57.40        19.53         3.48        11.05 
TCGA-24-2026 TCGA-24-2033 TCGA-25-1313 TCGA-25-1635 TCGA-25-1877 TCGA-25-2392 
       34.82        18.48        26.96        51.22        18.05         1.02 
TCGA-25-2396 TCGA-25-2398 TCGA-29-1691 TCGA-29-1761 TCGA-29-1770 TCGA-29-2432 
        3.02        45.01        47.18        17.00        24.36        11.84 
TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-36-1569 TCGA-36-1570 TCGA-36-1575 
       21.04        51.91         2.47        29.10        21.53         8.55 
TCGA-36-2529 TCGA-61-1728 TCGA-61-1733 TCGA-61-1740 TCGA-61-1743 TCGA-61-1915 
       35.05        27.88        31.79         2.43        43.69        67.76 
TCGA-61-1918 TCGA-61-2009 TCGA-61-2012 TCGA-61-2614 
       15.75        39.85        30.64         8.61 

$`4P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 
       18.51        11.87        65.52        63.09        48.76        63.98 
TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       65.46        32.52        44.32        76.57        71.47        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       56.55        41.59        19.99        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       48.89        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       45.37        29.16         9.47        57.76        17.98        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
        9.99        38.43        89.33        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       61.87        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
       97.55         6.18         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       63.09        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       81.47        18.51        33.24        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 
       35.44        35.80        15.12        19.86        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       39.58         2.73        12.39        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       55.17         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       32.25        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       28.70        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 
       43.86        35.28        35.28        13.61       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       74.27        66.67        70.39        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       48.33        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       34.06        29.98        21.17        14.89         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.08        10.88         6.61         7.36         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       61.71        98.04        20.68        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
       37.61        13.97        32.84        16.57         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.18         2.56         3.91         3.09        14.24        12.23 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 
       10.78         8.75         6.28        54.77        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       26.20        72.20        27.52        25.38        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
        2.93         2.66        47.54        42.54        40.54        15.39 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       31.76        49.41         8.81        29.13        18.90         2.24 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       51.35         3.22        31.20         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
      129.96         4.27         6.38        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        0.53        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
       49.84         2.76         4.70         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 
        0.76         6.25         6.02         5.95         5.36        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 
       19.17        18.67        43.53         8.55        72.92        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
      105.99         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 
       58.09        88.50        70.62        39.88        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       47.70        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       48.33        38.24         8.32         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
       11.28         5.79         5.52         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       16.44        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
      109.71        14.43        53.95        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86        53.26         1.02        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
        2.99        12.00         2.96        18.58        18.02        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
        0.36        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       35.54        14.96        24.99        85.05        13.02        49.05 
TCGA-25-2393 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
       38.04        12.00        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 
       31.00        26.99        78.90        44.71       101.79        38.53 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
        0.79        33.70        31.20        68.32         0.53        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       18.67        59.67        18.25        41.98        29.23        34.62 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
       85.68        66.81        62.93        39.12        31.23        22.98 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.55        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
        8.38         7.23         5.36        34.62        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 
       62.47        45.11         4.90        42.25        11.47         9.76 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       38.07        36.26        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1571 
        6.71        42.51        44.12         2.20        28.77        22.85 
TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
       22.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       21.60         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
        6.05        16.18        11.47         7.99        26.04        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
        9.44        42.02         7.46        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       11.38        21.14         1.74        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.02       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 
       34.39         2.14         5.42        44.81        20.52        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1734 
        8.09        20.94        31.43        18.54         4.34        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 
       48.79        44.84        35.80        33.67         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 
       37.05        42.51        48.92        56.61        43.43        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
        1.18        45.96        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87        20.68        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        6.35        31.07        39.68        18.94         0.79         8.05 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             1.02              0.26 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           119.08            180.20 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           25.135            28.735 
[1] "1.0 - 119.1 (25.1)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1.5"
D7V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  4P GAIN MUTATED         0    57                1
  4P GAIN WILD-TYPE       2   500                1
D7V3, multiclass
                  clus
vv                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         57               500
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, continuous
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  58
  4P GAIN WILD-TYPE   2 510
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   58
  4P GAIN WILD-TYPE    2  510
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1                 2
  YES              58               510
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  4P GAIN MUTATED    0  4  1  0
  4P GAIN WILD-TYPE 14 22  4  3
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               0                14
  R1               4                22
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     3
  4P GAIN WILD-TYPE                                3    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P GAIN MUTATED                           1
  4P GAIN WILD-TYPE                        31
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0    50
  4P GAIN WILD-TYPE                                         1   425
D7V7, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   3                15
  BLACK OR AFRICAN AMERICAN                               1                31
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  50               425
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     2  31
  4P GAIN WILD-TYPE   8 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2   31
  4P GAIN WILD-TYPE    8  294
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              31               294
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    13  19
  4Q GAIN WILD-TYPE 253 271
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               32               524 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               19               271 
$`4Q GAIN MUTATED`
TCGA-04-1349 TCGA-04-1356 TCGA-04-1525 TCGA-04-1530 TCGA-09-1668 TCGA-10-0936 
       21.57        49.28        38.37       119.08        55.36        35.80 
TCGA-13-0714 TCGA-13-0794 TCGA-13-0802 TCGA-13-0883 TCGA-13-0920 TCGA-13-2060 
        6.21        30.35         8.19        68.94        13.81         8.61 
TCGA-13-A5FU TCGA-20-1682 TCGA-23-2645 TCGA-24-1427 TCGA-24-1558 TCGA-24-1843 
        8.42        27.52         4.50         4.83        19.53         3.48 
TCGA-24-2026 TCGA-25-1313 TCGA-25-1877 TCGA-25-2396 TCGA-29-1691 TCGA-29-1701 
       34.82        26.96        18.05         3.02        47.18        16.90 
TCGA-29-1702 TCGA-29-1770 TCGA-29-2432 TCGA-30-1855 TCGA-36-1575 TCGA-61-1728 
       18.67        24.36        11.84         2.47         8.55        27.88 
TCGA-61-1743 TCGA-61-2012 
       43.69        30.64 

$`4Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 
       18.51        11.87        65.52        63.09        48.76        63.98 
TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       65.46        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 
       82.39        56.55        41.59        19.99        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       31.86        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       17.98        35.57         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       41.62        57.60        61.87        30.51        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        3.02         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        4.54       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       33.24        32.28        11.70         3.91        35.44        15.12 
TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
       19.86        24.59        44.55        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.10        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.38        11.54        34.06        32.25        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
        8.45        38.93        36.72        28.70        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
        7.79         8.12         8.28        43.86        35.28        35.28 
TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       13.61       107.18        91.40        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       61.84        67.99        69.01        43.36        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        7.36         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       20.68        22.39        70.82        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       38.20        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       13.97        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.18         2.56         3.91         3.09        14.24        12.23 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 
       10.78         8.75         6.28        54.77        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       26.20        72.20        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.66        47.54        42.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       31.76        49.41         8.81        29.13        18.90         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
       51.35        54.51         3.22        31.20        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       33.30        86.01       129.96         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       33.47        58.13         0.53        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 
       91.66        77.00        49.84         2.76         4.70         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.36        17.39        28.37        19.17        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
        8.55        72.92        12.46        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        3.45         1.18        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       16.21        56.58        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       88.50        70.62        39.88        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       38.24         8.32         3.72         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        5.79         5.52         9.80        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       11.05        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
      109.71        14.43        53.95        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       44.52        57.07        36.16         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       31.63        70.45        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 
       16.64        33.11        55.86        53.26         1.02        32.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       51.06        37.02         1.02        34.98        65.00        36.95 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       33.96         2.99        12.00         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       15.81         0.36        20.61         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 
       60.59        35.54        51.22        14.96        24.99        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 
       13.02        49.05         1.02        38.04        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        44.71       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       31.20        68.32         0.53        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       29.23        34.62        17.00        85.68        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       39.12        31.23        22.98        22.55        17.33        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       11.84        12.30        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       34.62        86.17        65.00        62.47        45.11         4.90 
TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       42.25        11.47         9.76        21.04        38.07        51.91 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 
       36.26        15.68         0.26        48.10        44.91        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
        6.12        36.62         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       42.51        44.12         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.85        22.55        30.08        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.69        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       20.52        14.17         6.05        16.18        11.47         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       26.04        23.74         9.44        42.02         7.46        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        1.48        24.03        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       29.00        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      116.12         9.40        34.39         2.14         5.42        44.81 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       20.52        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
        4.34        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
        2.43        33.67         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       13.02         9.07        34.13        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       48.92        56.61        67.76        43.43        15.75        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       39.85         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       51.72        71.74        61.64        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             2.47              0.26 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           119.08            180.20 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           20.550            28.735 
[1] "2.5 - 119.1 (20.6)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1.5"
D8V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  4Q GAIN MUTATED         0    32                0
  4Q GAIN WILD-TYPE       2   525                2
D8V3, multiclass
                  clus
vv                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         32               525
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, continuous
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  31
  4Q GAIN WILD-TYPE   2 537
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   31
  4Q GAIN WILD-TYPE    2  537
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1                 2
  YES              31               537
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  4Q GAIN MUTATED    0  1  1  0
  4Q GAIN WILD-TYPE 14 25  4  3
D8V6, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                46 
       TCGA-04-1516        TCGA-04-1644        TCGA-13-0807        TCGA-13-0911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-13-A5FT        TCGA-24-2033        TCGA-29-2414        TCGA-29-2425 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-29-2427        TCGA-29-2428        TCGA-29-2429        TCGA-29-2431 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-29-2434        TCGA-29-2436        TCGA-36-2529        TCGA-36-2530 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-36-2532        TCGA-36-2534        TCGA-36-2537        TCGA-36-2538 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-36-2540        TCGA-36-2542        TCGA-36-2543        TCGA-36-2544 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-36-2545        TCGA-36-2547        TCGA-36-2548        TCGA-36-2549 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-36-2551        TCGA-36-2552        TCGA-3P-A9WA        TCGA-42-2582 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-42-2587        TCGA-42-2588        TCGA-42-2589        TCGA-42-2590 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-42-2593        TCGA-57-1993        TCGA-59-2363        TCGA-59-2372 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-61-2612        TCGA-61-2613        TCGA-61-2614        TCGA-OY-A56P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-OY-A56Q        TCGA-VG-A8LO 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     2
  4Q GAIN WILD-TYPE                                3    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q GAIN MUTATED                           2
  4Q GAIN WILD-TYPE                        30
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0    26
  4Q GAIN WILD-TYPE                                         1   449
D8V7, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               2                30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  26               449
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  19
  4Q GAIN WILD-TYPE   9 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   19
  4Q GAIN WILD-TYPE    9  306
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              19               306
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    96  92
  5P GAIN WILD-TYPE 170 198
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              188               368 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               92               198 
$`5P GAIN MUTATED`
TCGA-04-1337 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 
        2.01        18.51        65.52        63.09        21.57        63.98 
TCGA-04-1364 TCGA-04-1530 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1654 
       33.67       119.08        84.20        27.88        64.64        47.70 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1661 TCGA-09-1666 TCGA-09-1670 
       57.76        17.98        35.57        38.43        57.60        17.98 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2054 TCGA-09-2056 TCGA-10-0927 
        8.55        97.55         6.18        20.94        12.46        81.47 
TCGA-10-0930 TCGA-10-0933 TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 TCGA-13-0725 
       33.24        11.70        35.80        24.59        39.58        12.39 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0766 
       15.19        17.82        55.17        11.18        11.54        21.40 
TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 TCGA-13-0801 TCGA-13-0883 TCGA-13-0886 
        8.45        36.72        30.35         8.28        68.94        74.27 
TCGA-13-0889 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       61.84        56.15        19.36        48.33        47.84        44.94 
TCGA-13-0911 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       27.72        10.88         6.61         6.05         5.92         6.84 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1484 TCGA-13-1488 TCGA-13-1492 TCGA-13-1498 
        4.21        87.06        98.04        70.82        73.55        37.61 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1512 
       32.84        16.57         4.21         4.41         4.77         3.09 
TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1685 TCGA-20-1686 
        8.75         8.42        25.94        26.20        16.70         2.93 
TCGA-23-1024 TCGA-23-1029 TCGA-23-1032 TCGA-23-1111 TCGA-23-1116 TCGA-23-1119 
       15.39         8.81         2.24         3.22         4.57       129.96 
TCGA-23-1121 TCGA-23-1809 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
        6.38         0.53        91.66        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1417 TCGA-24-1418 
        4.50        21.80        41.56        22.32         7.82         7.99 
TCGA-24-1423 TCGA-24-1425 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 TCGA-24-1469 
        6.25         5.95        17.39        18.67         8.55         9.11 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1549 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
        1.18        22.22        56.58        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1604 TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 
       39.88        88.37        38.24         3.72         3.81        11.28 
TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-2020 TCGA-24-2026 
        5.52        22.68        30.21        11.05       152.02        34.82 
TCGA-24-2030 TCGA-24-2260 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       53.95        36.16        47.54        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2295 TCGA-24-2298 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 
       67.36        33.11        53.26        34.98        65.00        33.96 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1627 TCGA-25-1631 TCGA-25-1634 
        2.99         2.96        18.58         0.36         0.30        35.54 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2396 TCGA-25-2404 TCGA-29-1688 
       18.05        85.05         1.02         3.02        29.03        78.90 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1707 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 
       47.18         0.79        41.98        17.00        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-2425 
       39.12        31.23        22.98        24.36        17.33        65.00 
TCGA-29-2432 TCGA-30-1718 TCGA-30-1853 TCGA-31-1950 TCGA-36-1568 TCGA-36-1569 
       11.84        51.91        36.26        18.77        28.77        29.10 
TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2543 TCGA-36-2548 
       30.08        27.85        24.69        35.05         2.24        14.17 
TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 
       16.18        26.04         9.44         1.48        24.03         1.74 
TCGA-57-1993 TCGA-59-A5PD TCGA-61-1725 TCGA-61-1733 TCGA-61-1899 TCGA-61-1903 
       25.08        20.52        31.43        31.79         8.42        13.02 
TCGA-61-1914 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
       56.61        15.75        38.17         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2087 TCGA-61-2098 TCGA-61-2101 TCGA-61-2111 TCGA-61-2612 
       30.64         4.80        65.52        55.50       125.75         6.35 
TCGA-61-2614 TCGA-OY-A56P 
        8.61        39.68 

$`5P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 
       40.24        41.00         1.81        49.15        46.62        11.87 
TCGA-04-1348 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
       48.76        65.46        49.28        32.52        44.32        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       71.47        82.39        56.55        41.59        19.99        38.37 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 
       29.10        55.43        48.89        28.64        36.23        31.86 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 
       45.37        29.16         9.47         9.99        89.33        74.93 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 
       41.62        61.87        55.36        30.51         5.85         3.02 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2055 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0931 
       39.75        26.93        54.31        25.91        18.51        32.28 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 
        3.91        35.44        15.12        19.86         6.21        44.55 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 
        2.73        31.10         2.50        11.38        34.06        32.25 
TCGA-13-0764 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       31.04        38.93        28.70        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.12         8.19        43.86        35.28        35.28        13.61 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 
      107.18        91.40        66.67        70.39        67.99        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0908 TCGA-13-0910 
       43.36        57.47        57.07        47.38        44.84        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 
       34.06        29.98        21.17        14.89        13.81         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1405 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
        6.41         6.08         7.36         4.70         5.33        54.64 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 
       61.71        29.42        20.68        22.39        82.88        52.44 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 
       38.20        49.25         4.24        54.31        38.40        13.97 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.91        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 
       10.78         6.28        54.77        23.05        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       25.38        19.10         2.66        47.54        42.54        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 
       26.83        31.76        49.41        29.13        18.90        51.35 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 
       54.51        31.20        68.68        33.30        86.01         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       39.09        33.47        58.13        24.95       115.89        87.48 
TCGA-23-2081 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0980 TCGA-24-1103 
       77.00         7.63        19.66        11.64         7.66        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 
       63.55        47.41         6.31         6.38         7.86         0.76 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        6.02         5.36         4.83        28.37        19.17        43.53 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1544 
       72.92        12.46        45.14       105.99         3.45        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        16.21        41.06        51.91        41.39 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 
       17.23        90.15        48.33         8.32         3.48         4.37 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 
        5.79         9.80        16.44        81.11         4.87        44.84 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       58.16       109.71        14.43        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2290 
       44.52        57.07         0.79         0.36        31.63        36.23 
TCGA-24-2293 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       16.64        55.86         1.02        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1323 TCGA-25-1625 TCGA-25-1626 
       37.02         1.02        36.95        12.00        18.02        15.81 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 
       20.61         7.86        56.94        60.59        51.22        14.96 
TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 
       24.99        13.02        49.05        38.04        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 
       19.99        42.02         2.96        31.00        26.99        44.71 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
      101.79        38.53        33.70        31.20        68.32         0.53 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 
       16.90        18.67        59.67        18.25        29.23        34.62 
TCGA-29-1762 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       85.68        22.55        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
        8.38         7.23         5.36        34.62        86.17        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11         4.90        42.25        11.47         9.76        21.04 
TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       38.07         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
       30.05        48.79        45.57        30.18        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       42.51        44.12         2.20        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
        8.55        25.74        24.23        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 
       25.91        25.08        23.80        21.60        20.98        18.31 
TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2589 
       20.52         6.05        11.47         7.99        23.74        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 
        7.46        40.77        11.38        21.14        22.32        29.00 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.02       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
       34.39         2.14         5.42        44.81        11.11         8.09 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 
       20.94        18.54        27.88         4.34        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       44.84        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
        5.79        11.41         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 
       42.51        48.92        67.76        43.43         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 
       14.50        17.98         1.18        45.96        45.40         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2102 
       51.72        71.74        61.64        58.39        60.62         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56Q 
       76.87        20.68        44.52        22.22        31.07        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.30              0.26 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           152.02            180.20 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           24.640            29.145 
[1] "0.3 - 152.0 (24.6)" "0.3 - 180.2 (29.1)"
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  5P GAIN MUTATED         0   189                2
  5P GAIN WILD-TYPE       2   368                0
D9V3, multiclass
                  clus
vv                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                        189               368
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, continuous
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1 194
  5P GAIN WILD-TYPE   2 374
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1  194
  5P GAIN WILD-TYPE    2  374
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                1                 2
  YES             194               374
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED    2  9  4  0
  5P GAIN WILD-TYPE 12 17  1  3
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0               2                12
  R1               9                17
  R2               4                 1
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  2     5
  5P GAIN WILD-TYPE                                1    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P GAIN MUTATED                          10
  5P GAIN WILD-TYPE                        22
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           1   161
  5P GAIN WILD-TYPE                                         0   314
D9V7, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 1
  ASIAN                                                   5                13
  BLACK OR AFRICAN AMERICAN                              10                22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 161               314
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3 107
  5P GAIN WILD-TYPE   7 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  107
  5P GAIN WILD-TYPE    7  218
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             107               218
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    29  27
  5Q GAIN WILD-TYPE 237 263
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               56               500 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               27               263 
$`5Q GAIN MUTATED`
TCGA-04-1337 TCGA-04-1347 TCGA-04-1349 TCGA-04-1364 TCGA-04-1530 TCGA-04-1542 
        2.01        63.09        21.57        33.67       119.08        84.20 
TCGA-09-0369 TCGA-09-1661 TCGA-09-1666 TCGA-09-1670 TCGA-10-0930 TCGA-10-0936 
       35.57        38.43        57.60        17.98        33.24        35.80 
TCGA-13-0751 TCGA-13-0768 TCGA-13-0792 TCGA-13-0911 TCGA-13-1409 TCGA-13-1492 
       55.17         8.45        36.72        27.72         6.84        73.55 
TCGA-13-1498 TCGA-13-1504 TCGA-13-2065 TCGA-13-A5FU TCGA-23-1111 TCGA-23-1116 
       37.61        16.57         8.75         8.42         3.22         4.57 
TCGA-23-2079 TCGA-23-2645 TCGA-24-1417 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 
       91.66         4.50         7.82        17.39        18.67         8.55 
TCGA-24-1471 TCGA-24-1556 TCGA-24-1604 TCGA-24-1845 TCGA-24-1850 TCGA-24-1923 
        1.18        70.62        88.37         3.81         5.52        22.68 
TCGA-24-2288 TCGA-24-2298 TCGA-25-1329 TCGA-25-1631 TCGA-25-2392 TCGA-29-1688 
        0.82        53.26         2.96         0.30         1.02        78.90 
TCGA-29-1763 TCGA-29-1769 TCGA-29-1770 TCGA-29-2432 TCGA-30-1853 TCGA-36-1569 
       66.81        22.98        24.36        11.84        36.26        29.10 
TCGA-36-2529 TCGA-36-2543 TCGA-36-2551 TCGA-61-1725 TCGA-61-1733 TCGA-61-2009 
       35.05         2.24        16.18        31.43        31.79        39.85 
TCGA-61-2612 TCGA-61-2614 
        6.35         8.61 

$`5Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00         1.81        49.15        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       11.87        65.52        48.76        63.98        65.46        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       32.52        44.32        76.57        71.47        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 
       41.59        19.99        38.37        29.10        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 
       45.37        29.16         9.47        57.76        17.98         9.99 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       89.33        74.93        41.62        61.87        55.36        30.51 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       35.15         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        54.31        25.91        81.47 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       18.51        32.28        11.70         3.91        35.44        15.12 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       19.86         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 
       12.39        31.10        15.19        17.82         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.38        11.54        34.06        32.25        31.04        21.40 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       38.93        28.70        30.35        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
        8.12         8.28         8.19        43.86        35.28        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       70.39        61.84        67.99        69.01        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       56.15        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.94        44.84        37.08        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       14.89        13.81         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 
        6.61         7.36         6.05         5.92         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 
       20.68        22.39        70.82        82.88        52.44        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       49.25         4.24        54.31        38.40        13.97        32.84 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.21         4.41         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 
        3.09        14.24        12.23         8.61        10.78         6.28 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
       54.77        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       42.54        40.54        15.39        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        8.81        29.13        18.90         2.24        51.35        54.51 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       31.20        68.68        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        6.38        39.09        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
      115.89        87.48        77.00        49.84         2.76         4.70 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 
        5.36         4.83        28.37        19.17        43.53        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 
       12.46        45.14       105.99         9.11         3.45        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 
       51.91        41.39        58.09        88.50        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       90.15        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 
        4.37        11.28         5.79         9.80        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       11.05        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       34.82       109.71        14.43        53.95        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       64.01        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 
       47.54        31.63        70.45        44.61        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       16.64        33.11        55.86         1.02        26.96        32.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       51.06        37.02         1.02        34.98        65.00        36.95 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       33.96         2.99        12.00        18.58        18.02        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
        0.36        20.61         7.86        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       51.22        14.96        24.99        18.05        85.05        13.02 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       49.05        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 
       42.02         2.96        29.03        31.00        26.99        44.71 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       47.18       101.79        38.53         0.79        33.70        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32         0.53        16.90        18.67        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 
       41.98        29.23        34.62        17.00        85.68        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       39.12        31.23        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        34.62 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       86.17        65.00        62.47        45.11         4.90        42.25 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       11.47         9.76        21.04        38.07        51.91         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       15.68         0.26        48.10        44.91        34.78         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       36.62         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       44.12         2.20        28.77        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        8.55        30.08        25.74        27.85        24.23        24.69 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
       21.60        20.98        18.31        20.52        14.17         6.05 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       11.47         7.99        26.04        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
        7.46        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.74        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
        5.42        44.81        20.52        11.11         8.09        20.94 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       18.54        27.88         4.34        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       35.80         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        4.01        30.64        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q 
       44.52       125.75        22.22        31.07        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.30              0.26 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           119.08            180.20 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           22.830            28.555 
[1] "0.3 - 119.1 (22.8)" "0.3 - 180.2 (28.6)"
[1] "hr=" "1"  
D10V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  5Q GAIN MUTATED         0    56                1
  5Q GAIN WILD-TYPE       2   501                1
D10V3, multiclass
                  clus
vv                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         56               501
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, continuous
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  59
  5Q GAIN WILD-TYPE   3 509
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   59
  5Q GAIN WILD-TYPE    3  509
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                 3
  YES              59               509
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED    0  7  1  0
  5Q GAIN WILD-TYPE 14 19  4  3
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0               0                14
  R1               7                19
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q GAIN MUTATED                           4
  5Q GAIN WILD-TYPE                        28
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    49
  5Q GAIN WILD-TYPE                                         1   426
D10V7, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               4                28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  49               426
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  27
  5Q GAIN WILD-TYPE  10 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   27
  5Q GAIN WILD-TYPE   10  298
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              27               298
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    84  77
  6P GAIN WILD-TYPE 182 213
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              161               395 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               77               213 
$`6P GAIN MUTATED`
TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1362 TCGA-04-1364 
       18.51        65.52        63.09        21.57        44.32        33.67 
TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-09-0364 TCGA-09-0366 
       41.59        38.37       119.08        29.10        29.16        57.76 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       38.43        89.33        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1674 TCGA-09-2049 TCGA-09-2051 TCGA-09-2054 TCGA-10-0930 
       30.51         8.55       112.41        63.09        20.94        33.24 
TCGA-10-0933 TCGA-13-0717 TCGA-13-0724 TCGA-13-0760 TCGA-13-0764 TCGA-13-0792 
       11.70        24.59         2.73        11.54        31.04        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0885 TCGA-13-0886 
       28.70        30.35        19.59         8.12        91.40        74.27 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       13.81         6.41         6.08         6.05         5.92         6.84 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1496 
        4.21        87.06        22.39        70.82        82.88         4.24 
TCGA-13-1499 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-20-0990 
       38.40         2.56        14.24         8.61        10.78        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-23-1023 TCGA-23-1031 
       26.20        27.52        16.70         2.93        40.54        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 
        2.24        51.35        54.51        68.68         4.57         4.27 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 TCGA-24-0982 TCGA-24-1417 TCGA-24-1423 
       58.13         0.53        91.66        22.32         7.82         6.25 
TCGA-24-1424 TCGA-24-1469 TCGA-24-1474 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 
        6.02         9.11        22.22        19.53        47.70        25.87 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1850 TCGA-24-2020 TCGA-24-2026 TCGA-24-2254 
       88.37        48.33         5.52       152.02        34.82        57.07 
TCGA-24-2261 TCGA-24-2267 TCGA-24-2281 TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 
        0.79        47.54        44.61         1.02        65.00        33.96 
TCGA-25-1323 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       12.00        35.54        14.96        24.99        18.05        85.05 
TCGA-25-2392 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-29-1691 
        1.02        45.01        42.02         2.96        29.03        47.18 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1710 TCGA-29-1764 
        0.79        68.32        16.90        18.67        29.23        62.93 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1778 TCGA-29-2414 TCGA-29-2425 TCGA-29-2432 
       24.36        17.33        14.93        86.17        65.00        11.84 
TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1856 TCGA-30-1861 TCGA-31-1953 TCGA-31-1955 
       21.04        51.91        15.68        34.78         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 
       44.12         2.20        22.85         8.55        30.08        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2542 TCGA-36-2545 TCGA-36-2551 TCGA-36-2552 
       24.69        35.05        21.60        18.31        16.18        11.47 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 
        1.48        24.03         1.74        22.32        25.08        25.02 
TCGA-61-1722 TCGA-61-1730 TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 TCGA-61-1907 
        8.09         4.34        44.84        33.67        43.69        31.30 
TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2003 TCGA-61-2009 
       67.76        15.75        38.17         5.52         4.01        39.85 
TCGA-61-2088 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2111 
        4.77        60.62        65.52         6.48        76.87       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56Q TCGA-WR-A838 
       22.22         6.35         8.61        18.94         8.05 

$`6P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       11.87        48.76        63.98        65.46        49.28        32.52 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1542 
       76.57        71.47        82.39        56.55        19.99        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 
       31.86        47.70        45.37         9.47        17.98        35.57 
TCGA-09-1659 TCGA-09-1664 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 
        9.99        74.93        17.98         5.85         3.02        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2053 
        6.18         6.12        35.15         4.54        71.11        39.75 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       32.28         3.91        35.44        35.80        15.12        19.86 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
        6.21        44.55        39.58        12.39        31.10        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 
       17.82        55.17         2.50        11.18        11.38        34.06 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0797 TCGA-13-0799 
       32.25        21.40         8.45        38.93         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        43.86        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       68.94       107.18        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       69.01        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       27.72        34.06        29.98        21.17        14.89         4.64 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
       10.88         6.61         7.36         4.70         5.33        54.64 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1491 TCGA-13-1492 
       61.71        29.42        98.04        20.68        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
       38.20        49.25        54.31        37.61        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 
       16.57         4.21         4.41         4.77         4.18         3.91 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        3.09        12.23         8.75         6.28        54.77         8.42 
TCGA-20-0987 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1021 
       23.05        72.20        25.38        19.10         2.66        47.54 
TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       42.54        15.39        26.83        31.76        49.41         8.81 
TCGA-23-1030 TCGA-23-1111 TCGA-23-1113 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       29.13         3.22        31.20        33.30        86.01       129.96 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
        6.38        39.09        33.47        24.95       115.89        87.48 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
       19.66        11.64        21.80        41.56         7.66        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 
       63.55        47.41         6.31         6.38         7.99         7.86 
TCGA-24-1422 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        0.76         5.95         5.36         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       19.17        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 
       45.14       105.99         3.45         1.18        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 
       58.09        88.50        70.62        39.88        44.09        45.50 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       10.26        17.23        90.15        38.24         8.32         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 
        3.72         3.81         4.37        11.28         5.79         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
       22.68        30.21        16.44        11.05        81.11         4.87 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       44.84        58.16       109.71        14.43        53.95        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 
       28.18        64.01        44.52        36.16         0.36        31.63 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       70.45         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       55.86        53.26         1.02        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
       37.02        34.98        36.95         2.99         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.02        15.81         0.36        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 
       56.94        60.59        51.22        13.02        49.05        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
        3.02        12.00        19.99        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 
       44.71       101.79        38.53        33.70        31.20         0.53 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       59.67        18.25        41.98        34.62        17.00        85.68 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 
       66.81        39.12        31.23        22.98        22.55        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       11.84        12.30         8.38         7.23         5.36        34.62 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 
       62.47        45.11         4.90        42.25        11.47         9.76 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       38.07        36.26         2.47         0.26        48.10        44.91 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
        6.12        36.62         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-36-1568 
       48.79        45.57        30.18        18.77        22.49        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-2530 
       29.10        21.53        22.55        25.74        27.85        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 
       29.49        29.82        25.91        25.08        23.80         2.24 
TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 
       20.98        20.52        14.17         6.05         7.99        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1583 
       23.74         9.44        42.02         7.46        40.77        11.38 
TCGA-57-1584 TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       21.14        29.00       180.20        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
        9.40        34.39         2.14         5.42        44.81        20.52 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 
       11.11        20.94        31.43        18.54        27.88        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 
       28.47        48.79        35.80         2.43         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 
        5.79        11.41        13.02         9.07        34.13        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1995 TCGA-61-2000 
       42.51        48.92        56.61        43.43         2.01        14.50 
TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       17.98        30.64        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 
        4.80        51.72        71.74        61.64        58.39        55.50 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2613 TCGA-OY-A56P TCGA-VG-A8LO 
       20.68        44.52        31.07        39.68         0.79 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.53              0.26 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           152.02            180.20 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            24.99             29.10 
[1] "0.5 - 152.0 (25.0)" "0.3 - 180.2 (29.1)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6P GAIN MUTATED         0   162                1
  6P GAIN WILD-TYPE       2   395                1
D11V3, multiclass
                  clus
vv                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                        162               395
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, continuous
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0 166
  6P GAIN WILD-TYPE   3 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0  166
  6P GAIN WILD-TYPE    3  402
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                0                 3
  YES             166               402
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  6P GAIN MUTATED    4  8  1  1
  6P GAIN WILD-TYPE 10 18  4  2
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               4                10
  R1               8                18
  R2               1                 4
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  2     2
  6P GAIN WILD-TYPE                                1    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P GAIN MUTATED                           8
  6P GAIN WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           0   142
  6P GAIN WILD-TYPE                                         1   333
D11V7, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 1
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               8                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 142               333
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2 100
  6P GAIN WILD-TYPE   8 225
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2  100
  6P GAIN WILD-TYPE    8  225
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO             100               225
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    50  43
  6Q GAIN WILD-TYPE 216 247
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               93               463 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               43               247 
$`6Q GAIN MUTATED`
TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1362 TCGA-04-1516 TCGA-04-1530 
       18.51        65.52        63.09        44.32        41.59       119.08 
TCGA-04-1536 TCGA-09-0364 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       29.10        29.16        41.62        61.87        55.36        30.51 
TCGA-09-1674 TCGA-09-2051 TCGA-10-0930 TCGA-10-0933 TCGA-13-0723 TCGA-13-0724 
        8.55        63.09        33.24        11.70        39.58         2.73 
TCGA-13-0760 TCGA-13-0764 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0885 
       11.54        31.04        30.35        19.59         8.12        91.40 
TCGA-13-0920 TCGA-13-0924 TCGA-13-1408 TCGA-13-1409 TCGA-13-1487 TCGA-13-1488 
       13.81         6.08         5.92         6.84        22.39        70.82 
TCGA-13-1496 TCGA-13-1499 TCGA-13-2057 TCGA-13-2061 TCGA-20-0991 TCGA-20-1682 
        4.24        38.40        14.24        10.78        26.20        27.52 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 TCGA-23-1124 
       54.51         3.22        68.68         4.57         4.27        58.13 
TCGA-23-1809 TCGA-23-2079 TCGA-24-1424 TCGA-24-1469 TCGA-24-1474 TCGA-24-1558 
        0.53        91.66         6.02         9.11        22.22        19.53 
TCGA-24-1563 TCGA-24-1604 TCGA-24-1614 TCGA-24-1850 TCGA-24-1928 TCGA-24-2267 
       47.70        88.37        48.33         5.52        11.05        47.54 
TCGA-24-2281 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 TCGA-25-2400 
       44.61        51.22        24.99        18.05         1.02        42.02 
TCGA-25-2404 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1702 TCGA-29-1710 
       29.03        47.18         0.79        68.32        18.67        29.23 
TCGA-29-1764 TCGA-29-1770 TCGA-29-1774 TCGA-29-1778 TCGA-29-2425 TCGA-30-1859 
       62.93        24.36        17.33        14.93        65.00        48.10 
TCGA-30-1861 TCGA-30-1862 TCGA-36-1575 TCGA-36-1576 TCGA-36-1581 TCGA-36-2551 
       34.78         6.12         8.55        30.08        24.69        16.18 
TCGA-36-2552 TCGA-57-1582 TCGA-57-1993 TCGA-57-1994 TCGA-61-1741 TCGA-61-1743 
       11.47        24.03        25.08        25.02        33.67        43.69 
TCGA-61-1915 TCGA-61-1919 TCGA-61-2003 TCGA-61-2088 TCGA-61-2102 TCGA-61-2111 
       67.76        38.17         4.01         4.77         6.48       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-WR-A838 
       22.22         6.35         8.05 

$`6Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1343 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       11.87        48.76        21.57        63.98        65.46        49.28 
TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       32.52        33.67        76.57        71.47        82.39        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       19.99        38.37        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       28.64        64.64        36.23        31.86        47.70        45.37 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
        9.47        57.76        17.98        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       89.33        74.93        57.60        17.98         5.85         3.02 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       97.55         6.18         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       71.11        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 
       25.91        81.47        18.51        32.28         3.91        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.80        15.12        19.86         6.21        24.59        44.55 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
       12.39        31.10        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 
       11.18        11.38        34.06        32.25        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       38.93        36.72        28.70         8.71         7.79         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.19        43.86        35.28        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      107.18        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       69.01        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       27.72        34.06        29.98        21.17        14.89         4.64 
TCGA-13-0923 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1410 
        6.41        10.88         6.61         7.36         6.05         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       98.04        20.68        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       49.25        54.31        37.61        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.21         4.41         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
        3.09        12.23         8.61         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
        8.42        23.05        25.94        72.20        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       16.70         2.93         2.66        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1113 TCGA-23-1117 TCGA-23-1118 
       18.90         2.24        51.35        31.20        33.30        86.01 
TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 
      129.96         6.38        39.09        33.47        24.95       115.89 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       87.48        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 
        7.82         7.99         7.86         0.76         6.25         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        5.36         4.83        17.39        28.37        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       43.53         8.55        72.92        12.46        45.14       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        3.45         1.18        26.96        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       56.58        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 
       70.62        39.88        44.09        45.50        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       17.23        90.15        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
        3.81         4.37        11.28         5.79         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       30.21        16.44        81.11         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       58.16        34.82       109.71        14.43        53.95        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       28.18        64.01        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
        0.36        31.63        70.45         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       16.64        33.11        55.86        53.26         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       32.02        51.06        37.02         1.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       36.95        33.96         2.99        12.00         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.02        15.81         0.36        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 
       56.94        60.59        35.54        14.96        85.05        13.02 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       49.05        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
        2.96        31.00        26.99        78.90        44.71       101.79 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 
       38.53        33.70        31.20         0.53        16.90        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       18.25        41.98        34.62        17.00        85.68        66.81 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 
       39.12        31.23        22.98        22.55        12.36        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       12.30         8.38         7.23         5.36        34.62        86.17 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       62.47        45.11         4.90        42.25        11.84        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
        9.76        21.04        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       15.68         0.26        44.91        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       22.49         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 
       29.10        21.53        22.85        22.55        25.74        27.85 
TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.23        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
       20.52        14.17         6.05         7.99        26.04        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 
        9.44        42.02         7.46        40.77         1.48        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 
       21.14         1.74        22.32        29.00       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       44.81        20.52        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       44.84        35.80         2.43         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 
       42.51        48.92        56.61        43.43        15.75         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
        5.52        14.50        17.98        30.64        39.85        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 
        1.18        45.96        45.40         4.80        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 
       61.64        58.39        60.62        65.52        55.50        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       20.68        44.52        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO 
        0.79 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.53              0.26 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           125.75            180.20 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            25.08             28.47 
[1] "0.5 - 125.8 (25.1)" "0.3 - 180.2 (28.5)"
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6Q GAIN MUTATED         0    94                0
  6Q GAIN WILD-TYPE       2   463                2
D12V3, multiclass
                  clus
vv                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         94               463
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, continuous
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  97
  6Q GAIN WILD-TYPE   3 471
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   97
  6Q GAIN WILD-TYPE    3  471
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                0                 3
  YES              97               471
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  6Q GAIN MUTATED    3  3  0  0
  6Q GAIN WILD-TYPE 11 23  5  3
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0               3                11
  R1               3                23
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  1     0
  6Q GAIN WILD-TYPE                                2    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q GAIN MUTATED                           5
  6Q GAIN WILD-TYPE                        27
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           0    84
  6Q GAIN WILD-TYPE                                         1   391
D12V7, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   0                18
  BLACK OR AFRICAN AMERICAN                               5                27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  84               391
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  54
  6Q GAIN WILD-TYPE   8 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   54
  6Q GAIN WILD-TYPE    8  271
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              54               271
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    84  90
  7P GAIN WILD-TYPE 182 200
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              174               382 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               90               200 
$`7P GAIN MUTATED`
TCGA-04-1337 TCGA-04-1342 TCGA-04-1346 TCGA-04-1351 TCGA-04-1364 TCGA-04-1367 
        2.01        18.51        65.52        65.46        33.67        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 
       56.55        19.99        84.20        48.89        27.88        64.64 
TCGA-04-1652 TCGA-09-0365 TCGA-09-0367 TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 
       31.86         9.47        17.98        38.43        41.62        61.87 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2049 
       17.98         5.85         8.55         6.18        35.15       112.41 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-10-0926 TCGA-13-0717 TCGA-13-0730 
       63.09        39.75        20.94        25.91        24.59        17.82 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 TCGA-13-0803 
       11.18        11.54        32.25         8.45        19.59        43.86 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0888 TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 
       13.61        68.94        70.39        56.15        19.36        47.38 
TCGA-13-0904 TCGA-13-0912 TCGA-13-0921 TCGA-13-0923 TCGA-13-1407 TCGA-13-1408 
       48.33        34.06         4.64         6.41         6.05         5.92 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 
        4.70         4.21        87.06        61.71        98.04        20.68 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1495 TCGA-13-1496 TCGA-13-1500 TCGA-13-1504 
       70.82        82.88        49.25         4.24        13.97        16.57 
TCGA-13-1509 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 
        4.18        12.23         8.61         8.42        23.05        26.20 
TCGA-20-1682 TCGA-20-1686 TCGA-20-1687 TCGA-23-1024 TCGA-23-1032 TCGA-23-1111 
       27.52         2.93         2.66        15.39         2.24         3.22 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        4.57        33.30         6.38        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-24-0980 TCGA-24-1413 TCGA-24-1418 
      115.89        91.66        77.00         7.66         6.31         7.99 
TCGA-24-1424 TCGA-24-1428 TCGA-24-1431 TCGA-24-1471 TCGA-24-1474 TCGA-24-1557 
        6.02        17.39        19.17         1.18        22.22        39.88 
TCGA-24-1558 TCGA-24-1564 TCGA-24-1614 TCGA-24-1845 TCGA-24-1850 TCGA-24-1928 
       19.53        25.87        48.33         3.81         5.52        11.05 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2038 TCGA-24-2261 TCGA-24-2267 
      152.02        34.82        53.95        44.52         0.79        47.54 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 
       70.45         0.82        16.64        33.11         1.02        26.96 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1323 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       34.98        36.95        12.00        15.81         0.36        20.61 
TCGA-25-1870 TCGA-25-1871 TCGA-25-2397 TCGA-25-2400 TCGA-29-1693 TCGA-29-1695 
       14.96        24.99        12.00        42.02       101.79         0.79 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1707 TCGA-29-1710 TCGA-29-1763 
       31.20        68.32         0.53        41.98        29.23        66.81 
TCGA-29-1764 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-2428 TCGA-29-2429 
       62.93        12.36        14.93         7.23        45.11         4.90 
TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1856 TCGA-30-1862 
       11.84        11.47        21.04        36.26        15.68         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-31-1950 TCGA-31-1959 TCGA-36-1580 TCGA-36-2547 
       36.62         1.22        18.77         2.20        24.23        20.52 
TCGA-36-2548 TCGA-42-2582 TCGA-42-2587 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 
       14.17        26.04        23.74        25.08       180.20        80.12 
TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
      116.12         2.14        44.81         4.34        31.79        28.47 
TCGA-61-1737 TCGA-61-1743 TCGA-61-1899 TCGA-61-1904 TCGA-61-1907 TCGA-61-1911 
       44.84        43.69         8.42         9.07        31.30        42.51 
TCGA-61-1914 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2088 TCGA-61-2098 
       56.61        15.75        38.17         4.01         4.77        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2113 TCGA-61-2614 
       55.50         6.48        76.87        44.52        22.22         8.61 

$`7P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 
       40.24        41.00         1.81        49.15        46.62        11.87 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 
       63.09        48.76        21.57        63.98        49.28        32.52 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 
       44.32        76.57        82.39        41.59        38.37       119.08 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 
       29.10        55.43        28.64        36.23        47.70        45.37 
TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 
       29.16        57.76        35.57         9.99        89.33        74.93 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 
       57.60        55.36        30.51         3.02        97.55         6.12 
TCGA-09-2048 TCGA-09-2050 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0927 
        4.54        71.11        26.93        12.46        54.31        81.47 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       18.51        33.24        32.28        11.70         3.91        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 
       35.80        15.12        19.86         6.21        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 
        2.73        12.39        31.10        15.19        55.17         2.50 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 
       11.38        34.06        31.04        21.40        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       28.70        30.35         8.71         7.79         8.12         8.28 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
        8.19        35.28        35.28       107.18        91.40        74.27 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       66.67        61.84        67.99        69.01        43.36        57.47 
TCGA-13-0900 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       57.07        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 
       29.98        21.17        14.89        13.81         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 
        6.61         7.36         6.84         5.33        54.64        29.42 
TCGA-13-1487 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 
       22.39        52.44        73.55        38.20        54.31        37.61 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 
       38.40        32.84         4.21         4.41         4.77         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
        3.91         3.09        14.24        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       54.77        25.94        72.20        25.38        19.10        16.70 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        42.54        40.54        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 
        8.81        29.13        18.90        51.35        54.51        31.20 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       68.68        86.01       129.96         4.27        39.09        33.47 
TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       87.48        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 
       19.66        11.64        21.80        41.56        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 
       63.55        47.41         6.38         7.82         7.86         0.76 
TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 
        6.25         5.95         5.36         4.83        28.37        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       43.53         8.55        72.92        12.46        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        9.11         3.45        26.96        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       56.58        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 
       70.62        44.09        45.50        47.70        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       90.15        88.37        38.24         8.32         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
        4.37        11.28         5.79         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 
       16.44        81.11         4.87        44.84        58.16       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 
       14.43        18.48        28.18        64.01        57.07        36.16 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 
        0.36        31.63        44.61        67.36        36.23        55.86 
TCGA-24-2298 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 
       53.26        32.02        51.06        37.02         1.02        65.00 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1630 
       33.96         2.99         2.96        18.58        18.02         7.86 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1877 
        0.30        56.94        60.59        35.54        51.22        18.05 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       85.05        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1696 TCGA-29-1701 
       78.90        44.71        47.18        38.53        33.70        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.67        59.67        18.25        34.62        17.00        85.68 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.12        31.23        22.98        24.36        22.55        17.33 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       11.84        12.30         8.38         5.36        34.62        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 
       65.00        62.47        42.25         9.76        38.07        51.91 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 
        2.47         0.26        48.10        44.91        34.78        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 
       24.26        30.05        48.79        45.57        30.18        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
        6.71        42.51        44.12        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.69        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2588 TCGA-42-2589 
        6.05        16.18        11.47         7.99         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
        7.46        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2350 TCGA-59-2352 
        1.74        22.32        29.00        25.02        22.32         9.40 
TCGA-59-2354 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
       34.39         5.42        20.52        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
       31.43        18.54        27.88        48.79        35.80         2.43 
TCGA-61-1741 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 
       33.67         1.45         5.79        11.41        13.02        34.13 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 
       37.05        48.92        67.76        43.43         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       14.50        17.98        30.64        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96        45.40         4.80        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2109 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 
       58.39        60.62        20.68       125.75         6.35        31.07 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       39.68        18.94         0.79         8.05 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.36              0.26 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           180.20            129.96 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           22.635            29.900 
[1] "0.4 - 180.2 (22.6)" "0.3 - 130.0 (29.9)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7P GAIN MUTATED         1   174                0
  7P GAIN WILD-TYPE       1   383                2
D13V3, multiclass
                  clus
vv                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  OMENTUM                        1                 1
  OVARY                        174               383
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, continuous
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     0 178
  7P GAIN WILD-TYPE   3 390
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      0  178
  7P GAIN WILD-TYPE    3  390
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                0                 3
  YES             178               390
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED    5  8  1  0
  7P GAIN WILD-TYPE  9 18  4  3
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0               5                 9
  R1               8                18
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  0     2
  7P GAIN WILD-TYPE                                3    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED                           6
  7P GAIN WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           1   157
  7P GAIN WILD-TYPE                                         0   318
D13V7, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               6                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 157               318
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     1 107
  7P GAIN WILD-TYPE   9 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1  107
  7P GAIN WILD-TYPE    9  218
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO             107               218
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    88 102
  7Q GAIN WILD-TYPE 178 188
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              190               366 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              102               188 
$`7Q GAIN MUTATED`
TCGA-04-1337 TCGA-04-1342 TCGA-04-1347 TCGA-04-1351 TCGA-04-1364 TCGA-04-1514 
        2.01        18.51        63.09        65.46        33.67        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 
       41.59        19.99        29.10        84.20        48.89        27.88 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-0365 TCGA-09-0367 TCGA-09-1661 
       64.64        31.86        45.37         9.47        17.98        38.43 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       41.62        61.87        17.98         5.85         8.55         6.18 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2053 TCGA-10-0926 TCGA-10-0927 TCGA-13-0717 
       35.15        63.09        39.75        25.91        81.47        24.59 
TCGA-13-0724 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 
        2.73        11.18        11.54        32.25         8.45        19.59 
TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0888 
       43.86        35.28        13.61        68.94        91.40        70.39 
TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0912 TCGA-13-0921 
       56.15        19.36        47.38        48.33        34.06         4.64 
TCGA-13-0923 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 
        6.41         6.05         4.70         4.21         5.33        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-13-1495 
       61.71        98.04        20.68        70.82        82.88        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1500 TCGA-13-1504 TCGA-13-1509 TCGA-13-2059 
        4.24        54.31        13.97        16.57         4.18        12.23 
TCGA-13-2060 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-1682 TCGA-20-1686 
        8.61         8.42        23.05        26.20        27.52         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1031 TCGA-23-1032 TCGA-23-1111 
        2.66        47.54        15.39        18.90         2.24         3.22 
TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
      129.96         6.38        39.09         0.53        24.95       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-24-1104 TCGA-24-1413 TCGA-24-1418 TCGA-24-1424 
       91.66        77.00        63.55         6.31         7.99         6.02 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 TCGA-24-1471 TCGA-24-1474 TCGA-24-1546 
       17.39        19.17         8.55         1.18        22.22        64.27 
TCGA-24-1548 TCGA-24-1557 TCGA-24-1558 TCGA-24-1614 TCGA-24-1844 TCGA-24-1845 
       16.21        39.88        19.53        48.33         3.72         3.81 
TCGA-24-1850 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 
        5.52        11.05         4.87       152.02        34.82        53.95 
TCGA-24-2033 TCGA-24-2038 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 
       18.48        44.52         0.79         0.36        47.54        70.45 
TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1318 TCGA-25-1320 
       33.11         1.02        26.96        32.02        34.98        36.95 
TCGA-25-1323 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1870 
       12.00        18.58        15.81         0.36        20.61        14.96 
TCGA-25-1871 TCGA-25-1878 TCGA-25-2397 TCGA-25-2400 TCGA-25-2401 TCGA-29-1695 
       24.99        85.05        12.00        42.02         2.96         0.79 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1707 TCGA-29-1764 TCGA-29-1775 
       31.20        68.32         0.53        41.98        62.93        12.36 
TCGA-29-1778 TCGA-29-1783 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 
       14.93         7.23        45.11         4.90        11.84        11.47 
TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-31-1950 
       21.04        36.26         6.12        36.62         1.22        18.77 
TCGA-36-1580 TCGA-36-2529 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-42-2582 
       24.23        35.05        18.31        20.52        14.17        26.04 
TCGA-42-2587 TCGA-42-2590 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 
       23.74         7.46        22.32        25.08       180.20        80.12 
TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 TCGA-61-1725 TCGA-61-1730 TCGA-61-1733 
      116.12         2.14        44.81        31.43         4.34        31.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1743 TCGA-61-1899 TCGA-61-1901 TCGA-61-1904 
       44.84         2.43        43.69         8.42        11.41         9.07 
TCGA-61-1906 TCGA-61-1911 TCGA-61-1914 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 
       34.13        42.51        56.61        15.75        38.17         4.01 
TCGA-61-2088 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2113 
        4.77        55.50         6.48        76.87        44.52        22.22 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
        8.61        39.68        18.94         8.05 

$`7Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 
       40.24        41.00         1.81        49.15        46.62        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 
       65.52        48.76        21.57        63.98        49.28        32.52 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1525 TCGA-04-1530 
       44.32        76.57        71.47        82.39        38.37       119.08 
TCGA-04-1638 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 TCGA-09-0366 
       55.43        28.64        36.23        47.70        29.16        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 
       35.57         9.99        89.33        74.93        57.60        55.36 
TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 
       30.51         3.02        97.55         6.12         4.54       112.41 
TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0928 
       71.11        20.94        26.93        12.46        54.31        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       33.24        32.28        11.70         3.91        35.44        35.80 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       15.12        19.86         6.21        44.55        39.58        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 
       31.10        15.19        17.82        55.17         2.50        11.38 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       34.06        31.04        21.40        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       30.35         8.71         7.79         8.12         8.28         8.19 
TCGA-13-0804 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 
       35.28       107.18        74.27        66.67        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0905 TCGA-13-0906 
       69.01        43.36        57.47        57.07        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       44.84        37.08        27.72        29.98        21.17        14.89 
TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 
       13.81         6.08        10.88         6.61         7.36         5.92 
TCGA-13-1409 TCGA-13-1477 TCGA-13-1483 TCGA-13-1487 TCGA-13-1491 TCGA-13-1492 
        6.84        54.64        29.42        22.39        52.44        73.55 
TCGA-13-1494 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 
       38.20        37.61        38.40        32.84         4.21         4.41 
TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 
        4.77         2.56         3.91         3.09        14.24        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 
        8.75         6.28        54.77        25.94        72.20        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 
       19.10        16.70        42.54        40.54        26.83        31.76 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 
       49.41         8.81        29.13        51.35        54.51        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1123 
       68.68         4.57        33.30        86.01         4.27        33.47 
TCGA-23-1124 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       58.13        87.48        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 
       22.32        54.12        47.41         6.38         7.82         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 
        0.76         6.25         5.95         5.36         4.83        28.37 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       18.67        43.53        72.92        12.46        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1549 TCGA-24-1550 
        9.11         3.45        26.96        57.40        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 
       51.91        41.39        58.09        88.50        70.62        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 
       88.37        38.24         8.32         3.48         4.37        11.28 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 
        5.79         9.80        22.68        30.21        16.44        81.11 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 
       44.84        58.16       109.71        14.43        28.18        64.01 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       57.07        36.16        31.63        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1315 TCGA-25-1316 
       36.23        16.64        55.86        53.26        51.06        37.02 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1625 
        1.02        65.00        33.96         2.99         2.96        18.02 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
        7.86         0.30        56.94        60.59        35.54        51.22 
TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       18.05        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       45.01        19.99        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1701 
       44.71        47.18       101.79        38.53        33.70        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       18.67        59.67        18.25        29.23        34.62        17.00 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       85.68        66.81        39.12        31.23        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 
       22.55        17.33        11.84        12.30         8.38         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 
       34.62        86.17        65.00        62.47        42.25         9.76 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       38.07        51.91         2.47        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       44.91        34.78        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       45.57        30.18        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 
        8.55        30.08        25.74        27.85        24.69        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
        2.24        20.98         6.05        16.18        11.47         7.99 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
        9.44        42.02        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1994 TCGA-59-2350 TCGA-59-2352 
       21.14         1.74        29.00        25.02        22.32         9.40 
TCGA-59-2354 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
       34.39         5.42        20.52        11.11         8.09        20.94 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 TCGA-61-1741 
       18.54        27.88        28.47        48.79        35.80        33.67 
TCGA-61-1895 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 
        1.45         5.79        13.02        31.30        37.05        48.92 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       67.76        43.43         2.01         5.52        14.50        17.98 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       30.64        39.85        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.80        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2109 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-VG-A8LO 
       65.52        20.68       125.75         6.35        31.07         0.79 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.36              0.26 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           180.20            125.75 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           22.270            29.655 
[1] "0.4 - 180.2 (22.3)" "0.3 - 125.8 (29.7)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7Q GAIN MUTATED         0   193                1
  7Q GAIN WILD-TYPE       2   364                1
D14V3, multiclass
                  clus
vv                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                        193               364
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, continuous
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     0 198
  7Q GAIN WILD-TYPE   3 370
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      0  198
  7Q GAIN WILD-TYPE    3  370
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                0                 3
  YES             198               370
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED    7 11  2  1
  7Q GAIN WILD-TYPE  7 15  3  2
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0               7                 7
  R1              11                15
  R2               2                 3
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     2
  7Q GAIN WILD-TYPE                                3    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED                           8
  7Q GAIN WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           1   168
  7Q GAIN WILD-TYPE                                         0   307
D14V7, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               8                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 168               307
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     3 116
  7Q GAIN WILD-TYPE   7 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3  116
  7Q GAIN WILD-TYPE    7  209
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             116               209
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    51  64
  8P GAIN WILD-TYPE 215 226
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              115               441 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               64               226 
$`8P GAIN MUTATED`
TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       18.51        11.87        63.09        21.57        63.98        65.46 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1542 TCGA-09-0365 TCGA-09-0369 TCGA-09-1659 
       44.32        33.67        84.20         9.47        35.57         9.99 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1672 TCGA-09-2043 TCGA-10-0935 TCGA-10-0937 
       41.62        61.87         5.85         6.18        35.44        15.12 
TCGA-13-0717 TCGA-13-0724 TCGA-13-0726 TCGA-13-0751 TCGA-13-0768 TCGA-13-0794 
       24.59         2.73        31.10        55.17         8.45        30.35 
TCGA-13-0800 TCGA-13-0884 TCGA-13-0893 TCGA-13-0897 TCGA-13-0903 TCGA-13-0908 
        8.12       107.18        43.36        57.47        47.38        44.84 
TCGA-13-0911 TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 TCGA-13-1485 TCGA-13-1488 
       27.72         6.61         5.92         6.84        20.68        70.82 
TCGA-13-1497 TCGA-13-1506 TCGA-13-2057 TCGA-13-2060 TCGA-13-2071 TCGA-20-0987 
       54.31         4.41        14.24         8.61         6.28        23.05 
TCGA-20-1683 TCGA-20-1687 TCGA-23-1023 TCGA-23-1029 TCGA-23-1109 TCGA-23-1110 
       25.38         2.66        40.54         8.81        51.35        54.51 
TCGA-23-1111 TCGA-23-1119 TCGA-23-2079 TCGA-24-0979 TCGA-24-1103 TCGA-24-1418 
        3.22       129.96        91.66        41.56        54.12         7.99 
TCGA-24-1435 TCGA-24-1471 TCGA-24-1545 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 
       43.53         1.18        57.40        58.09        70.62        39.88 
TCGA-24-1563 TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 TCGA-24-2019 TCGA-24-2020 
       47.70        11.28         5.79        22.68         4.87       152.02 
TCGA-24-2262 TCGA-24-2271 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1329 
        0.36        31.63         1.02         1.02        36.95         2.96 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1632 TCGA-25-1877 TCGA-25-2392 
       18.58        18.02        20.61        56.94        18.05         1.02 
TCGA-25-2398 TCGA-25-2401 TCGA-29-1690 TCGA-29-1693 TCGA-29-1696 TCGA-29-1702 
       45.01         2.96        44.71       101.79        33.70        18.67 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1776 TCGA-29-1777 TCGA-29-1785 TCGA-29-2425 
       66.81        62.93        11.84        12.30        34.62        65.00 
TCGA-29-2431 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1861 TCGA-30-1892 
       42.25        38.07        51.91        36.26        34.78        48.79 
TCGA-31-1946 TCGA-31-1956 TCGA-31-1959 TCGA-36-1576 TCGA-36-2529 TCGA-36-2548 
       30.18        44.12         2.20        30.08        35.05        14.17 
TCGA-36-2551 TCGA-42-2582 TCGA-57-1582 TCGA-59-2354 TCGA-59-2355 TCGA-61-1743 
       16.18        26.04        24.03        34.39         2.14        43.69 
TCGA-61-1899 TCGA-61-1906 TCGA-61-2009 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 
        8.42        34.13        39.85       125.75         6.35         8.61 
TCGA-OY-A56Q 
       18.94 

$`8P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1356 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 
       65.52        48.76        49.28        32.52        76.57        71.47 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        41.59        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       29.10        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 
       36.23        31.86        47.70        45.37        29.16        57.76 
TCGA-09-0367 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 
       17.98        38.43        89.33        74.93        57.60        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 
       30.51        17.98         3.02         8.55        97.55         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       35.15         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        54.31        25.91        81.47 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 
       18.51        33.24        32.28        11.70         3.91        35.80 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 
       19.86         6.21        44.55        39.58        12.39        15.19 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       17.82         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       32.25        31.04        21.40        38.93        36.72        28.70 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       19.59         8.71         7.79         8.28         8.19        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 
       35.28        35.28        13.61        68.94        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0899 
       66.67        70.39        61.84        67.99        69.01        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       57.07        19.36        48.33        47.84        44.94        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 
       34.06        29.98        21.17        14.89        13.81         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1410 
        6.41         6.08        10.88         7.36         6.05         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       98.04        22.39        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       49.25         4.24        37.61        38.40        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       16.57         4.21         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
        3.09        12.23        10.78         8.75        54.77         8.42 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
       25.94        26.20        72.20        27.52        19.10        16.70 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.93        47.54        42.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1113 TCGA-23-1114 
       49.41        29.13        18.90         2.24        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
        4.57        33.30        86.01         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       33.47        58.13         0.53        24.95       115.89        87.48 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 
       19.66        11.64        21.80         7.66        22.32        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 
       47.41         6.31         6.38         7.82         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       28.37        19.17        18.67         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 
       45.14       105.99         9.11         3.45        22.22        26.96 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 
       88.50        19.53        44.09        45.50        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1850 TCGA-24-1920 
        3.48         3.72         3.81         4.37         5.52         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 
       30.21        16.44        11.05        81.11        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       34.82       109.71        14.43        53.95        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
       64.01        44.52        57.07        36.16         0.79        47.54 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86        53.26        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       37.02        34.98        65.00        33.96         2.99        12.00 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 
       15.81         0.36         7.86         0.30        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       51.22        14.96        24.99        85.05        13.02        49.05 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 
       38.04         3.02        12.00        19.99        42.02        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 
       31.00        26.99        78.90        47.18        38.53         0.79 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32         0.53        16.90        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1766 
       41.98        29.23        34.62        17.00        85.68        39.12 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       31.23        22.98        24.36        22.55        17.33        12.36 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2427 
       14.93         8.38         7.23         5.36        86.17        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11         4.90        11.84        11.47         9.76        21.04 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 
        2.47        15.68         0.26        48.10        44.91         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 
       36.62         1.22        57.57        24.26        30.05        45.57 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-36-1568 TCGA-36-1569 
       18.77        22.49         6.71        42.51        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 
       21.53        22.85        22.55         8.55        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.23        24.69        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2588 
       20.52         6.05        11.47         7.99        23.74         9.44 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 
       42.02         7.46        40.77         1.48        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.74        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 
       80.12        22.32       116.12         9.40         5.42        44.81 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       20.52        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 
       35.80         2.43        33.67         1.45         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       13.02         9.07        31.30        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       56.61        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 
        5.52        14.50        17.98         4.01        30.64        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
        1.18        45.96        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 
        6.48        76.87        20.68        44.52        22.22        31.07 
TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
       39.68         0.79         8.05 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.36              0.26 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           152.02            180.20 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            30.35             27.85 
[1] "0.4 - 152.0 (30.4)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8P GAIN MUTATED         0   115                1
  8P GAIN WILD-TYPE       2   442                1
D15V3, multiclass
                  clus
vv                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                        115               442
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, continuous
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1 116
  8P GAIN WILD-TYPE   2 452
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1  116
  8P GAIN WILD-TYPE    2  452
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                1                 2
  YES             116               452
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED    2  7  0  1
  8P GAIN WILD-TYPE 12 19  5  2
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0               2                12
  R1               7                19
  R2               0                 5
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     1
  8P GAIN WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P GAIN MUTATED                           6
  8P GAIN WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           0   104
  8P GAIN WILD-TYPE                                         1   371
D15V7, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               6                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 104               371
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2  69
  8P GAIN WILD-TYPE   8 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   69
  8P GAIN WILD-TYPE    8  256
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              69               256
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   104 130
  8Q GAIN WILD-TYPE 162 160
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              234               322 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              130               160 
$`8Q GAIN MUTATED`
TCGA-04-1335 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 
        1.81        46.62        18.51        11.87        63.09        21.57 
TCGA-04-1351 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1530 TCGA-04-1536 
       65.46        44.32        33.67        76.57       119.08        29.10 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1652 TCGA-09-0365 TCGA-09-1659 TCGA-09-1661 
       84.20        27.88        31.86         9.47         9.99        38.43 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 
       41.62        61.87        55.36        17.98         5.85         8.55 
TCGA-09-2043 TCGA-10-0925 TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 TCGA-10-0935 
        6.18        54.31        81.47        33.24        11.70        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0724 TCGA-13-0726 
       35.80        15.12        19.86        24.59         2.73        31.10 
TCGA-13-0751 TCGA-13-0761 TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 TCGA-13-0800 
       55.17        34.06         8.45        36.72        30.35         8.12 
TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0890 TCGA-13-0893 
        8.19        13.61        68.94       107.18        67.99        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0911 TCGA-13-0919 
       57.47        56.15        57.07        47.38        27.72        14.89 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.08        10.88         6.61         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1497 TCGA-13-1500 
        4.21        98.04        20.68        70.82        54.31        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-2059 
       32.84        16.57         4.21         4.41         4.77        12.23 
TCGA-13-2060 TCGA-13-2071 TCGA-20-0987 TCGA-20-0991 TCGA-20-1683 TCGA-20-1686 
        8.61         6.28        23.05        26.20        25.38         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1029 TCGA-23-1031 
        2.66        42.54        40.54        26.83         8.81        18.90 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 
       51.35        54.51         3.22         4.57        33.30       129.96 
TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 
        6.38        33.47        58.13        24.95       115.89        91.66 
TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0979 TCGA-24-1103 
       49.84         4.70         4.50        21.80        41.56        54.12 
TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
       47.41         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1467 TCGA-24-1471 
       18.67        43.53         8.55        12.46       105.99         1.18 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       57.40        64.27        56.58        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 TCGA-24-1844 
       70.62        39.88        19.53        47.70        25.87         3.72 
TCGA-24-1847 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-2019 TCGA-24-2020 
       11.28        22.68        30.21        16.44         4.87       152.02 
TCGA-24-2027 TCGA-24-2033 TCGA-24-2035 TCGA-24-2262 TCGA-24-2271 TCGA-24-2290 
      109.71        18.48        28.18         0.36        31.63        36.23 
TCGA-24-2295 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 TCGA-25-1329 
       33.11         1.02         1.02        36.95        33.96         2.96 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1632 TCGA-25-1877 
       18.58        18.02         0.36        20.61        56.94        18.05 
TCGA-25-1878 TCGA-25-2392 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 
       85.05         1.02         3.02        45.01        19.99         2.96 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       44.71       101.79        38.53         0.79        33.70        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1763 
       68.32         0.53        16.90        18.67        59.67        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       62.93        39.12        17.33        11.84        12.30        14.93 
TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 
        7.23        34.62        65.00        62.47        42.25        11.84 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 
       38.07        51.91        36.26         0.26        48.10        34.78 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       24.26        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 
       44.12         2.20        29.10        21.53        22.55        30.08 
TCGA-36-1580 TCGA-36-2529 TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-3P-A9WA 
       24.23        35.05         2.24        14.17        16.18         7.99 
TCGA-42-2582 TCGA-42-2588 TCGA-57-1582 TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 
       26.04         9.44        24.03         1.74        22.32       180.20 
TCGA-59-2354 TCGA-59-2355 TCGA-61-1725 TCGA-61-1728 TCGA-61-1736 TCGA-61-1741 
       34.39         2.14        31.43        27.88        48.79        33.67 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       43.69         8.42        34.13        31.30        37.05        42.51 
TCGA-61-1914 TCGA-61-1919 TCGA-61-1998 TCGA-61-2009 TCGA-61-2016 TCGA-61-2088 
       56.61        38.17         5.52        39.85         1.18         4.77 
TCGA-61-2109 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO 
       20.68       125.75         6.35         8.61        18.94         0.79 

$`8Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1346 TCGA-04-1348 
       40.24        41.00        49.15         2.01        65.52        48.76 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       63.98        49.28        32.52        71.47        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       41.59        19.99        38.37        55.43        48.89        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 
       64.64        36.23        47.70        45.37        29.16        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1669 
       17.98        35.57        89.33        74.93        57.60        30.51 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
        3.02        97.55         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-10-0926 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-13-0714 TCGA-13-0720 
       25.91        18.51        32.28         3.91         6.21        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 
       39.58        12.39        15.19        17.82         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 
       11.38        11.54        32.25        31.04        21.40        38.93 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 
       28.70        19.59         8.71         7.79         8.28        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       35.28        35.28        91.40        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       61.84        69.01        19.36        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       44.84        37.08        34.06        29.98        21.17        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-1405 TCGA-13-1407 TCGA-13-1412 TCGA-13-1477 
        4.64         6.41         7.36         6.05         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 
       87.06        61.71        29.42        22.39        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 
       73.55        38.20        49.25         4.24        37.61        38.40 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 
        4.18         2.56         3.91         3.09        14.24        10.78 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 
        8.75        54.77         8.42        25.94        72.20        27.52 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 
       19.10        16.70        47.54        15.39        31.76        49.41 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 TCGA-23-1120 
       29.13         2.24        31.20        68.68        86.01         4.27 
TCGA-23-1122 TCGA-23-1809 TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 
       39.09         0.53        87.48        77.00         2.76         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 
       19.66        11.64         7.66        22.32        63.55         6.31 
TCGA-24-1416 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.38         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 
       28.37        19.17        72.92        45.14         9.11         3.45 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1560 
       22.22        26.96        16.21        41.06        51.91        44.09 
TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       45.50        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 
       38.24         8.32         3.48         3.81         4.37         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1928 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 
        5.52         9.80        11.05        81.11        44.84        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       34.82        14.43        53.95        64.01        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       36.16         0.79        47.54        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 
       67.36        16.64        55.86        53.26        26.96        32.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1322 TCGA-25-1323 
       51.06        37.02        34.98        65.00         2.99        12.00 
TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       15.81         7.86         0.30        60.59        35.54        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 
       14.96        24.99        13.02        49.05        38.04        12.00 
TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 
       42.02        29.03        31.00        26.99        78.90        47.18 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        29.23        34.62        17.00        85.68 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1781 
       31.23        22.98        24.36        22.55        12.36         8.38 
TCGA-29-1784 TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 
        5.36        86.17        45.11         4.90        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1856 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 
       21.04         2.47        15.68        44.91         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-31-1953 TCGA-31-1955 TCGA-36-1568 
        1.22        57.57        30.05         6.71        42.51        28.77 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 
       22.85         8.55        25.74        27.85        24.69        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-42-2587 
       20.98        18.31        20.52         6.05        11.47        23.74 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 
       42.02         7.46        40.77         1.48        11.38        21.14 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       29.00        25.08        25.02        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 
        9.40         5.42        44.81        20.52        11.11         8.09 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 
       20.94        18.54         4.34        31.79        28.47        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       35.80         2.43         1.45         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 
        9.07        48.92        67.76        43.43        15.75         2.01 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2017 
       14.50        17.98         4.01        30.64        30.64        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.40         4.80        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 
       60.62        65.52        55.50         6.48        76.87        44.52 
TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56P TCGA-WR-A838 
       22.22        31.07        39.68         8.05 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.26              0.30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           180.20            116.12 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           26.515            28.735 
[1] "0.3 - 180.2 (26.5)" "0.3 - 116.1 (28.7)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8Q GAIN MUTATED         1   234                2
  8Q GAIN WILD-TYPE       1   323                0
D16V3, multiclass
                  clus
vv                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  OMENTUM                        1                 1
  OVARY                        234               323
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, continuous
D16V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     1 238
  8Q GAIN WILD-TYPE   2 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1  238
  8Q GAIN WILD-TYPE    2  330
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                1                 2
  YES             238               330
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED    2 12  2  2
  8Q GAIN WILD-TYPE 12 14  3  1
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0               2                12
  R1              12                14
  R2               2                 3
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     4
  8Q GAIN WILD-TYPE                                3    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q GAIN MUTATED                          14
  8Q GAIN WILD-TYPE                        18
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           0   207
  8Q GAIN WILD-TYPE                                         1   268
D16V7, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   4                14
  BLACK OR AFRICAN AMERICAN                              14                18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 207               268
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3 139
  8Q GAIN WILD-TYPE   7 186
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  139
  8Q GAIN WILD-TYPE    7  186
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             139               186
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    37  49
  9P GAIN WILD-TYPE 229 241
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               86               470 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               49               241 
$`9P GAIN MUTATED`
TCGA-04-1362 TCGA-04-1516 TCGA-04-1655 TCGA-09-1668 TCGA-09-2045 TCGA-09-2051 
       44.32        41.59        45.37        55.36        35.15        63.09 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-13-0723 TCGA-13-0730 TCGA-13-0751 
       11.70        35.44        35.80        39.58        17.82        55.17 
TCGA-13-0803 TCGA-13-0807 TCGA-13-0884 TCGA-13-0893 TCGA-13-0911 TCGA-13-0919 
       43.86        13.61       107.18        43.36        27.72        14.89 
TCGA-13-0923 TCGA-13-1488 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1511 
        6.41        70.82        16.57         4.21         4.77         3.91 
TCGA-20-0990 TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1024 TCGA-23-1026 
       25.94        25.38         2.93         2.66        15.39        26.83 
TCGA-23-1032 TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2077 TCGA-23-2084 
        2.24         6.38        39.09         0.53       115.89        49.84 
TCGA-24-0968 TCGA-24-1424 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 TCGA-24-1466 
       19.66         6.02        17.39        18.67         8.55        45.14 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 TCGA-24-1552 TCGA-24-1553 
        9.11         1.18        26.96        16.21        41.39        58.09 
TCGA-24-1556 TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 TCGA-24-1850 TCGA-24-1924 
       70.62         8.32         3.72        11.28         5.52        30.21 
TCGA-24-1928 TCGA-24-2020 TCGA-24-2026 TCGA-24-2288 TCGA-24-2298 TCGA-25-1319 
       11.05       152.02        34.82         0.82        53.26        65.00 
TCGA-25-1320 TCGA-25-1329 TCGA-25-1628 TCGA-25-1635 TCGA-25-1878 TCGA-25-2396 
       36.95         2.96        20.61        51.22        85.05         3.02 
TCGA-25-2404 TCGA-29-1762 TCGA-29-1763 TCGA-29-1777 TCGA-29-1784 TCGA-30-1855 
       29.03        85.68        66.81        12.30         5.36         2.47 
TCGA-30-1859 TCGA-30-1862 TCGA-30-1867 TCGA-36-1577 TCGA-36-1581 TCGA-36-2532 
       48.10         6.12         1.22        25.74        24.69        29.49 
TCGA-36-2543 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1906 TCGA-61-2087 
        2.24        33.67        43.69         1.45        34.13         4.80 
TCGA-61-2094 TCGA-61-2111 
       71.74       125.75 

$`9P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 
       63.98        65.46        49.28        32.52        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       71.47        82.39        56.55        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       29.10        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 
       64.64        36.23        31.86        47.70        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 
       74.93        41.62        57.60        61.87        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        4.54       112.41        71.11        39.75        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        54.31        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       32.28         3.91        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 
       44.55         2.73        12.39        31.10        15.19         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       11.18        11.38        11.54        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       19.59         8.71         7.79         8.12         8.28         8.19 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       35.28        35.28        68.94        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 
       70.39        61.84        67.99        69.01        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       44.84        37.08        34.06        29.98        21.17        13.81 
TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        4.64         6.08        10.88         6.61         7.36         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        5.92         6.84         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       87.06        61.71        29.42        98.04        20.68        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1506 
       54.31        37.61        38.40        13.97        32.84         4.41 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.09        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       10.78         8.75         6.28        54.77         8.42        23.05 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 
       26.20        72.20        27.52        19.10        16.70        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       42.54        40.54        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
       18.90        51.35        54.51         3.22        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 
        4.57        33.30        86.01       129.96         4.27        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 
       58.13        24.95        87.48        91.66        77.00         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.70         4.50         7.63        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        5.95         5.36         4.83        28.37        19.17        43.53 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1545 
       72.92        12.46       105.99         3.45        22.22        57.40 
TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1557 
       64.27        56.58        41.06        51.91        88.50        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 
       17.23        90.15        88.37        48.33        38.24         3.48 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 
        3.81         4.37         5.79         9.80        22.68        16.44 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
       81.11         4.87        44.84        58.16       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       53.95        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
       44.61        67.36        36.23        16.64        33.11        55.86 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        32.02        51.06        37.02         1.02 
TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 
       34.98        33.96         2.99        12.00        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       15.81         0.36         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 
       35.54        14.96        24.99        18.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
        1.02        38.04        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
        2.96        31.00        26.99        78.90        44.71        47.18 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
        0.53        16.90        18.67        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       29.23        34.62        17.00        62.93        39.12        31.23 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
       14.93         8.38         7.23        34.62        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       62.47        45.11         4.90        42.25        11.84        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 
        9.76        21.04        38.07        51.91        36.26        15.68 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 
        0.26        44.91        34.78        36.62        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
        6.71        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 
       21.53        22.85        22.55         8.55        30.08        27.85 
TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.23        35.05        33.01        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       23.80        21.60        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
        6.05        16.18        11.47         7.99        26.04        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
        9.44        42.02         7.46        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       11.38        21.14         1.74        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.02       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 
       34.39         2.14         5.42        44.81        20.52        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
        8.09        20.94        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       31.79        28.47        48.79        44.84        35.80         2.43 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 
        8.42         5.79        11.41        13.02         9.07        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
        4.01        30.64        39.85        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
       45.40         4.77        51.72        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.53              0.26 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           152.02            180.20 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            25.84             28.67 
[1] "0.5 - 152.0 (25.8)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1.1"
D17V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  9P GAIN MUTATED         0    87                0
  9P GAIN WILD-TYPE       2   470                2
D17V3, multiclass
                  clus
vv                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         87               470
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, continuous
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  87
  9P GAIN WILD-TYPE   2 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   87
  9P GAIN WILD-TYPE    2  481
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                 2
  YES              87               481
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  9P GAIN MUTATED    2  3  0  0
  9P GAIN WILD-TYPE 12 23  5  3
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0               2                12
  R1               3                23
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  1     3
  9P GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P GAIN MUTATED                           5
  9P GAIN WILD-TYPE                        27
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           0    73
  9P GAIN WILD-TYPE                                         1   402
D17V7, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   3                15
  BLACK OR AFRICAN AMERICAN                               5                27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  73               402
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     0  50
  9P GAIN WILD-TYPE  10 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   50
  9P GAIN WILD-TYPE   10  275
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              50               275
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    20  22
  9Q GAIN WILD-TYPE 246 268
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               42               514 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               22               268 
$`9Q GAIN MUTATED`
TCGA-04-1362 TCGA-04-1516 TCGA-09-1668 TCGA-13-0723 TCGA-13-0761 TCGA-13-0887 
       44.32        41.59        55.36        39.58        34.06        66.67 
TCGA-13-0893 TCGA-13-0911 TCGA-13-0919 TCGA-13-1505 TCGA-20-1683 TCGA-20-1687 
       43.36        27.72        14.89         4.21        25.38         2.66 
TCGA-23-1032 TCGA-23-1122 TCGA-23-1809 TCGA-23-2084 TCGA-24-1428 TCGA-24-1434 
        2.24        39.09         0.53        49.84        17.39        18.67 
TCGA-24-1436 TCGA-24-1466 TCGA-24-1552 TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 
        8.55        45.14        41.39         8.32         3.72        11.28 
TCGA-24-1850 TCGA-24-2020 TCGA-24-2298 TCGA-25-1329 TCGA-25-1628 TCGA-25-1635 
        5.52       152.02        53.26         2.96        20.61        51.22 
TCGA-25-1878 TCGA-25-2404 TCGA-29-1762 TCGA-29-1784 TCGA-30-1855 TCGA-30-1862 
       85.05        29.03        85.68         5.36         2.47         6.12 
TCGA-31-1959 TCGA-36-1577 TCGA-36-2542 TCGA-42-2591 TCGA-61-1740 TCGA-61-2008 
        2.20        25.74        21.60        40.77         2.43        30.64 

$`9Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 
       63.98        65.46        49.28        32.52        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       71.47        82.39        56.55        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       29.10        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 
       64.64        36.23        31.86        47.70        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
        9.47        57.76        17.98        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 
       89.33        74.93        41.62        57.60        61.87        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       17.98         5.85         3.02         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       39.75        20.94        26.93        12.46        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       81.47        18.51        33.24        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       35.44        35.80        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55         2.73        12.39        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 
       55.17         2.50        11.18        11.38        11.54        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       30.35        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.19        43.86        35.28        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        74.27        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       69.01        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 
       48.33        47.84        44.94        44.84        37.08        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        13.81         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       10.88         6.61         7.36         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
        4.70         4.21         5.33        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       29.42        98.04        20.68        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 
       37.61        38.40        13.97        32.84        16.57         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
        4.77         4.18         2.56         3.91         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       12.23         8.61        10.78         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.42        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       19.10        16.70         2.93        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
       18.90        51.35        54.51         3.22        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
        4.57        33.30        86.01       129.96         4.27         6.38 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13        24.95       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 
       77.00         2.76         4.70         4.50         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.86         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 
        4.83        28.37        19.17        43.53        72.92        12.46 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
      105.99         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 
       88.37        48.33        38.24         3.48         3.81         4.37 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.79         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
       81.11         4.87        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       14.43        53.95        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86         1.02        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
        2.99        12.00        18.58        18.02        15.81         0.36 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 
        7.86         0.30        56.94        60.59        35.54        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       24.99        18.05        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
        3.02        12.00        45.01        19.99        42.02         2.96 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
       31.00        26.99        78.90        44.71        47.18       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       38.53         0.79        33.70        31.20        68.32         0.53 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       16.90        18.67        59.67        18.25        41.98        29.23 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       34.62        17.00        66.81        62.93        39.12        31.23 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 
       12.30        14.93         8.38         7.23        34.62        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       65.00        62.47        45.11         4.90        42.25        11.84 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       11.47         9.76        21.04        38.07        51.91        36.26 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 
       15.68         0.26        48.10        44.91        34.78        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       28.77        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       30.08        27.85        24.23        24.69        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 
       29.49        29.82        25.91        25.08        23.80         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       20.98        18.31        20.52        14.17         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       11.47         7.99        26.04        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
        7.46         1.48        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       44.81        20.52        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       44.84        35.80        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        4.01        39.85        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       39.68        18.94         0.79         8.05 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.53              0.26 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           152.02            180.20 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            25.56             28.42 
[1] "0.5 - 152.0 (25.6)" "0.3 - 180.2 (28.4)"
[1] "hr=" "1.1"
D18V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  9Q GAIN MUTATED         0    42                0
  9Q GAIN WILD-TYPE       2   515                2
D18V3, multiclass
                  clus
vv                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         42               515
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, continuous
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  42
  9Q GAIN WILD-TYPE   2 526
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   42
  9Q GAIN WILD-TYPE    2  526
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                 2
  YES              42               526
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  9Q GAIN MUTATED    1  2  0  0
  9Q GAIN WILD-TYPE 13 24  5  3
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               1                13
  R1               2                24
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  1     3
  9Q GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q GAIN MUTATED                           2
  9Q GAIN WILD-TYPE                        30
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           0    36
  9Q GAIN WILD-TYPE                                         1   439
D18V7, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   3                15
  BLACK OR AFRICAN AMERICAN                               2                30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  36               439
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  25
  9Q GAIN WILD-TYPE  10 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   25
  9Q GAIN WILD-TYPE   10  300
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              25               300
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    87  94
  10P GAIN WILD-TYPE 179 196
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               181                375 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                94                196 
$`10P GAIN MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 
       41.00        46.62        11.87        65.52        63.09        21.57 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1517 TCGA-04-1530 TCGA-04-1542 
       63.98        49.28        44.32        19.99       119.08        84.20 
TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-0365 TCGA-09-0369 
       27.88        64.64        31.86        45.37         9.47        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
        9.99        38.43        61.87        55.36        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2050 TCGA-09-2051 TCGA-10-0930 TCGA-10-0933 
        3.02         8.55        71.11        63.09        33.24        11.70 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0762 TCGA-13-0768 
       15.19        17.82        55.17        11.18        32.25         8.45 
TCGA-13-0802 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0888 TCGA-13-0890 
        8.19        13.61       107.18        91.40        70.39        67.99 
TCGA-13-0911 TCGA-13-0919 TCGA-13-0923 TCGA-13-1407 TCGA-13-1409 TCGA-13-1411 
       27.72        14.89         6.41         6.05         6.84         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 
        5.33        54.64        87.06        73.55        49.25         4.24 
TCGA-13-1499 TCGA-13-1504 TCGA-13-2060 TCGA-13-2061 TCGA-20-0987 TCGA-20-1682 
       38.40        16.57         8.61        10.78        23.05        27.52 
TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 
       25.38        16.70         2.93        47.54        42.54        15.39 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1116 TCGA-23-1122 TCGA-23-1123 
       18.90         2.24        54.51         4.57        39.09        33.47 
TCGA-23-1124 TCGA-23-2077 TCGA-23-2643 TCGA-24-0982 TCGA-24-1417 TCGA-24-1418 
       58.13       115.89         4.70        22.32         7.82         7.99 
TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 TCGA-24-1469 
        6.02         4.83        17.39        18.67         8.55         9.11 
TCGA-24-1544 TCGA-24-1548 TCGA-24-1564 TCGA-24-1565 TCGA-24-1616 TCGA-24-1843 
       26.96        16.21        25.87        10.26        38.24         3.48 
TCGA-24-1850 TCGA-24-1928 TCGA-24-2020 TCGA-24-2260 TCGA-24-2261 TCGA-24-2281 
        5.52        11.05       152.02        36.16         0.79        44.61 
TCGA-24-2293 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       16.64         1.02         1.02        36.95        33.96         2.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
        2.96        18.58        15.81         0.36        20.61         0.30 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 TCGA-29-1691 
       35.54        51.22        24.99        18.05         1.02        47.18 
TCGA-29-1693 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 TCGA-29-1763 
      101.79        16.90        18.67        59.67        29.23        66.81 
TCGA-29-1766 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 
       39.12        12.36        12.30        14.93         7.23        34.62 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ 
       86.17        65.00        45.11        11.84         9.76        21.04 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1861 TCGA-30-1866 TCGA-30-1887 TCGA-31-1950 
       36.26        15.68        34.78        36.62        24.26        18.77 
TCGA-31-1953 TCGA-36-1569 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
        6.71        29.10        25.74        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2588 
       35.05         2.24        14.17        16.18        11.47         9.44 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       24.03        11.38        22.32        25.08        25.02       180.20 
TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        9.40        44.81         8.09        27.88         4.34        31.79 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1904 TCGA-61-1907 TCGA-61-1911 TCGA-61-1917 
        2.43        33.67         9.07        31.30        42.51        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2012 TCGA-61-2018 TCGA-61-2098 
       15.75        38.17         4.01        30.64        45.40        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2111 TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q 
       55.50         6.48       125.75         6.35        39.68        18.94 
TCGA-WR-A838 
        8.05 

$`10P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1348 
       40.24         1.81        49.15         2.01        18.51        48.76 
TCGA-04-1351 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       65.46        32.52        33.67        76.57        71.47        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 
       56.55        41.59        38.37        29.10        55.43        48.89 
TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 
       28.64        36.23        47.70        29.16        57.76        17.98 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1675 
       89.33        74.93        41.62        57.60        30.51        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 
        6.18         6.12        35.15         4.54       112.41        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        54.31        25.91        81.47 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       18.51        32.28         3.91        35.44        35.80        15.12 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       19.86         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       12.39        31.10         2.50        11.38        11.54        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       31.04        21.40        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 
       19.59         8.71         7.79         8.12         8.28        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       35.28        35.28        68.94        74.27        66.67        61.84 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       69.01        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 
       34.06        29.98        21.17        13.81         4.64         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1410 TCGA-13-1482 
       10.88         6.61         7.36         5.92         4.70        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       29.42        98.04        20.68        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
       52.44        38.20        54.31        37.61        13.97        32.84 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.21         4.41         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
        3.09        14.24        12.23         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1684 TCGA-20-1687 
        8.42        25.94        26.20        72.20        19.10         2.66 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 
       51.35         3.22        31.20        68.68        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 
      129.96         4.27         6.38         0.53        24.95        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 
       91.66        77.00        49.84         2.76         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
       19.66        11.64        21.80        41.56         7.66        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 
       63.55        47.41         6.31         6.38         7.86         0.76 
TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        6.25         5.95         5.36        28.37        19.17        43.53 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 
       72.92        12.46        45.14       105.99         3.45         1.18 
TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       22.22        57.40        64.27        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       44.09        45.50        47.70        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       48.33         8.32         3.72         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 
        5.79         9.80        22.68        30.21        16.44        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
        4.87        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       53.95        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 
        0.36        47.54        31.63        70.45         0.82        67.36 
TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 
       36.23        33.11        55.86        53.26        26.96        32.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1323 TCGA-25-1625 
       51.06        37.02        34.98        65.00        12.00        18.02 
TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 
        7.86        56.94        60.59        14.96        85.05        13.02 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       49.05        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       42.02         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
       44.71        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1699 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
        0.53        18.25        41.98        34.62        17.00        85.68 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       62.93        31.23        22.98        24.36        22.55        17.33 
TCGA-29-1776 TCGA-29-1781 TCGA-29-1784 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
       11.84         8.38         5.36        62.47         4.90        42.25 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 
       11.47        38.07        51.91         2.47         0.26        48.10 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
       44.91         6.12         1.22        57.57        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       45.57        30.18        22.49        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       28.77        21.53        22.85        22.55         8.55        30.08 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-3P-A9WA 
       21.60        20.98        18.31        20.52         6.05         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       26.04        23.74        42.02         7.46        40.77         1.48 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       21.14         1.74        29.00        80.12        22.32       116.12 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 
       34.39         2.14         5.42        20.52        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       31.43        18.54        28.47        48.79        44.84        35.80 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       43.69         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1906 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1995 
       34.13        37.05        48.92        56.61        67.76         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 
        5.52        14.50        17.98        30.64        39.85         1.18 
TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 
       58.39        60.62        76.87        20.68        44.52        22.22 
TCGA-61-2613 TCGA-61-2614 TCGA-VG-A8LO 
       31.07         8.61         0.79 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.30               0.26 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            180.20             129.96 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             23.05              30.08 
[1] "0.3 - 180.2 (23.1)" "0.3 - 130.0 (30.1)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10P GAIN MUTATED         1   180                2
  10P GAIN WILD-TYPE       1   377                0
D19V3, multiclass
                  clus
vv                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         180                377
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, continuous
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2 183
  10P GAIN WILD-TYPE   1 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2  183
  10P GAIN WILD-TYPE    1  385
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                  1
  YES              183                385
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  10P GAIN MUTATED    4 11  2  1
  10P GAIN WILD-TYPE 10 15  3  2
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0                4                 10
  R1               11                 15
  R2                2                  3
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     4
  10P GAIN WILD-TYPE                                3    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P GAIN MUTATED                           8
  10P GAIN WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           0   162
  10P GAIN WILD-TYPE                                         1   313
D19V7, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                8                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  162                313
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2 108
  10P GAIN WILD-TYPE   8 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2  108
  10P GAIN WILD-TYPE    8  217
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO              108                217
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    48  58
  10Q GAIN WILD-TYPE 218 232
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               106                450 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                58                232 
$`10Q GAIN MUTATED`
TCGA-04-1332 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1517 
       41.00        21.57        63.98        49.28        44.32        19.99 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 TCGA-09-0365 
      119.08        84.20        27.88        31.86        45.37         9.47 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 
        9.99        38.43        55.36        17.98         5.85         8.55 
TCGA-09-2055 TCGA-10-0930 TCGA-10-0933 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 
       26.93        33.24        11.70        15.19        17.82        11.18 
TCGA-13-0762 TCGA-13-0802 TCGA-13-0884 TCGA-13-0885 TCGA-13-0890 TCGA-13-0919 
       32.25         8.19       107.18        91.40        67.99        14.89 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1495 TCGA-13-1504 TCGA-13-2061 
       54.64        87.06        98.04        49.25        16.57        10.78 
TCGA-20-0990 TCGA-20-1682 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1110 
       25.94        27.52        16.70        47.54        42.54        54.51 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 TCGA-23-2643 TCGA-24-0982 TCGA-24-1424 
       33.47        58.13       115.89         4.70        22.32         6.02 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1548 TCGA-24-1564 TCGA-24-1616 TCGA-24-2019 
        4.83        17.39        16.21        25.87        38.24         4.87 
TCGA-24-2020 TCGA-24-2261 TCGA-24-2293 TCGA-25-1312 TCGA-25-1317 TCGA-25-1318 
      152.02         0.79        16.64         1.02         1.02        34.98 
TCGA-25-1321 TCGA-25-1623 TCGA-25-1626 TCGA-25-1631 TCGA-25-1634 TCGA-25-1877 
       33.96        18.58        15.81         0.30        35.54        18.05 
TCGA-25-2392 TCGA-29-1702 TCGA-29-1710 TCGA-29-1763 TCGA-29-1775 TCGA-29-1777 
        1.02        18.67        29.23        66.81        12.36        12.30 
TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ 
        7.23        65.00        45.11        11.84         9.76        21.04 
TCGA-30-1853 TCGA-30-1861 TCGA-30-1866 TCGA-31-1950 TCGA-36-1578 TCGA-36-1580 
       36.26        34.78        36.62        18.77        27.85        24.23 
TCGA-36-2529 TCGA-36-2548 TCGA-36-2552 TCGA-57-1582 TCGA-57-1583 TCGA-57-1994 
       35.05        14.17        11.47        24.03        11.38        25.02 
TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 TCGA-61-1741 
        9.40        44.81         8.09         4.34        31.79        33.67 
TCGA-61-1904 TCGA-61-1907 TCGA-61-1915 TCGA-61-2003 TCGA-61-2098 TCGA-61-2101 
        9.07        31.30        67.76         4.01        65.52        55.50 
TCGA-61-2111 TCGA-61-2612 TCGA-OY-A56Q TCGA-WR-A838 
      125.75         6.35        18.94         8.05 

$`10Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24         1.81        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1351 TCGA-04-1361 
       11.87        65.52        63.09        48.76        65.46        32.52 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       33.67        76.57        71.47        82.39        56.55        41.59 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 
       38.37        29.10        55.43        48.89        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       36.23        47.70        29.16        57.76        17.98        35.57 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 
       89.33        74.93        41.62        57.60        61.87        30.51 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        3.02        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 
      112.41        71.11        63.09        39.75        20.94        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 
       54.31        25.91        81.47        18.51        32.28         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       35.44        35.80        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0751 
       44.55        39.58         2.73        12.39        31.10        55.17 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
        2.50        11.38        11.54        34.06        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
        8.45        38.93        36.72        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
        8.71         7.79         8.12         8.28        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       35.28        13.61        68.94        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       61.84        69.01        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36        47.38        48.33        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       37.08        27.72        34.06        29.98        21.17        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       61.71        29.42        20.68        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       52.44        73.55        38.20         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       38.40        13.97        32.84         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.18         2.56         3.91         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
        8.61         8.75         6.28        54.77         8.42        23.05 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 
       26.20        72.20        25.38        19.10         2.93         2.66 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        31.76        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 
       29.13        18.90         2.24        51.35         3.22        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       68.68         4.57        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 
        6.38        39.09         0.53        24.95        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 
       77.00        49.84         2.76         4.50         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
       11.64        21.80        41.56         7.66        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 
        0.76         6.25         5.95         5.36        28.37        19.17 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
      105.99         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       45.50        47.70        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       48.33         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
       11.28         5.79         5.52         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       16.44        11.05        81.11        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
      109.71        14.43        53.95        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       44.52        57.07        36.16         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 
       70.45        44.61         0.82        67.36        36.23        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26        26.96        32.02        51.06        37.02 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 
       65.00        36.95         2.99        12.00         2.96        18.02 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 
        0.36        20.61         7.86        56.94        60.59        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 
       14.96        24.99        85.05        13.02        49.05        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
        3.02        12.00        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
       29.03        31.00        26.99        78.90        44.71        47.18 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
        0.53        16.90        59.67        18.25        41.98        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
       17.00        85.68        62.93        39.12        31.23        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 
       24.36        22.55        17.33        11.84        14.93         8.38 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
        5.36        34.62        86.17        62.47         4.90        42.25 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       11.47        38.07        51.91         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       48.10        44.91         6.12         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
       30.05        48.79        45.57        30.18        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       42.51        44.12         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1581 
       22.85        22.55         8.55        30.08        25.74        24.69 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 
       21.60         2.24        20.98        18.31        20.52         6.05 
TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       16.18         7.99        26.04        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        7.46        40.77         1.48        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       29.00        25.08       180.20        80.12        22.32       116.12 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 
       34.39         2.14         5.42        20.52        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       31.43        18.54        27.88        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       35.80         2.43        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       11.41        13.02        34.13        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       56.61        43.43        15.75        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       14.50        17.98        30.64        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       61.64        58.39        60.62         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO 
       44.52        22.22        31.07         8.61        39.68         0.79 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.30               0.26 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            152.02             180.20 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            24.625             29.015 
[1] "0.3 - 152.0 (24.6)" "0.3 - 180.2 (29.0)"
[1] "hr=" "1"  
D20V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10Q GAIN MUTATED         1   105                1
  10Q GAIN WILD-TYPE       1   452                1
D20V3, multiclass
                  clus
vv                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         105                452
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, continuous
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0 108
  10Q GAIN WILD-TYPE   3 460
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0  108
  10Q GAIN WILD-TYPE    3  460
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 0                  3
  YES              108                460
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  10Q GAIN MUTATED    3  6  0  1
  10Q GAIN WILD-TYPE 11 20  5  2
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                3                 11
  R1                6                 20
  R2                0                  5
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     2
  10Q GAIN WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED                           4
  10Q GAIN WILD-TYPE                        28
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           0    94
  10Q GAIN WILD-TYPE                                         1   381
D20V7, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                4                 28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   94                381
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  59
  10Q GAIN WILD-TYPE   8 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   59
  10Q GAIN WILD-TYPE    8  266
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               59                266
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    42  33
  11P GAIN WILD-TYPE 224 257
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                75                481 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                33                257 
$`11P GAIN MUTATED`
TCGA-04-1343 TCGA-04-1346 TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 TCGA-04-1516 
       11.87        65.52        63.98        32.52        44.32        41.59 
TCGA-09-0369 TCGA-09-2043 TCGA-09-2051 TCGA-10-0931 TCGA-13-0724 TCGA-13-0727 
       35.57         6.18        63.09        32.28         2.73        15.19 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 
       19.59         8.71        91.40        66.67        70.39        67.99 
TCGA-13-1407 TCGA-13-1410 TCGA-13-1497 TCGA-13-1499 TCGA-13-2057 TCGA-23-1021 
        6.05         4.70        54.31        38.40        14.24        47.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1111 
       15.39        26.83         8.81        29.13        51.35         3.22 
TCGA-23-1116 TCGA-23-1119 TCGA-23-2072 TCGA-23-2084 TCGA-23-2645 TCGA-24-1417 
        4.57       129.96        24.95        49.84         4.50         7.82 
TCGA-24-1434 TCGA-24-1471 TCGA-24-1548 TCGA-24-1551 TCGA-24-1556 TCGA-24-1564 
       18.67         1.18        16.21        51.91        70.62        25.87 
TCGA-24-1604 TCGA-24-1842 TCGA-24-1844 TCGA-24-1850 TCGA-24-1928 TCGA-24-2030 
       88.37         8.32         3.72         5.52        11.05        53.95 
TCGA-25-1312 TCGA-25-1321 TCGA-25-1322 TCGA-25-1635 TCGA-25-1877 TCGA-25-2400 
        1.02        33.96         2.99        51.22        18.05        42.02 
TCGA-29-1691 TCGA-29-1701 TCGA-29-1774 TCGA-29-1775 TCGA-29-1783 TCGA-30-1718 
       47.18        16.90        17.33        12.36         7.23        51.91 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 
        2.47         0.26        48.10        22.55        30.08        27.85 
TCGA-42-2587 TCGA-59-2348 TCGA-59-2351 TCGA-61-1740 TCGA-61-1907 TCGA-61-1915 
       23.74       180.20       116.12         2.43        31.30        67.76 
TCGA-61-2012 TCGA-61-2097 TCGA-OY-A56P 
       30.64        60.62        39.68 

$`11P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 
       18.51        63.09        48.76        21.57        65.46        49.28 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       33.67        76.57        71.47        82.39        56.55        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       38.37       119.08        29.10        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 
       45.37        29.16         9.47        57.76        17.98         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       38.43        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       55.36        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
       97.55         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       39.75        20.94        26.93        12.46        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       81.47        18.51        33.24        11.70         3.91        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.80        15.12        19.86         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
       39.58        12.39        31.10        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       11.18        11.38        11.54        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        7.79         8.12         8.28         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0889 
       35.28        13.61        68.94       107.18        74.27        61.84 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       69.01        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        5.92         6.84         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       61.71        29.42        98.04        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        13.97        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
        4.77         4.18         2.56         3.91         3.09        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        8.61        10.78         8.75         6.28        54.77         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       23.05        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 
       19.10        16.70         2.93         2.66        42.54        40.54 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1113 
       31.76        49.41        18.90         2.24        54.51        31.20 
TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       68.68        33.30        86.01         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13         0.53       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
       77.00         2.76         4.70         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
       47.41         6.31         6.38         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       28.37        19.17        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 
       45.14       105.99         9.11         3.45        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 
       57.40        64.27        56.58        41.06        41.39        58.09 
TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       88.50        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 
       10.26        17.23        90.15        48.33        38.24         3.48 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
        3.81         4.37        11.28         5.79         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       30.21        16.44        81.11         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 
       58.16        34.82       109.71        14.43        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       64.01        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       47.54        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 
       36.23        16.64        33.11        55.86        53.26        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       32.02        51.06        37.02         1.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       36.95        12.00         2.96        18.58        18.02        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
        0.36        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       35.54        14.96        24.99        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
        1.02        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        44.71 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
        0.53        18.67        59.67        18.25        41.98        29.23 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       34.62        17.00        85.68        66.81        62.93        39.12 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 
       31.23        22.98        24.36        22.55        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
       14.93         8.38         5.36        34.62        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       62.47        45.11         4.90        42.25        11.84        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1860 
        9.76        21.04        38.07        36.26        15.68        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
        6.71        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 
       21.53        22.85         8.55        25.74        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       23.80        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 
       14.17         6.05        16.18        11.47         7.99        26.04 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
        9.44        42.02         7.46        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       11.38        21.14         1.74        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       25.02        80.12        22.32         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
        5.42        44.81        20.52        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       31.43        18.54        27.88         4.34        31.79        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       48.79        44.84        35.80        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 
       37.05        42.51        48.92        56.61        43.43        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       30.64        39.85         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
        4.77        51.72        71.74        61.64        58.39        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO 
       22.22         6.35        31.07         8.61        18.94         0.79 
TCGA-WR-A838 
        8.05 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.26               0.30 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            180.20             152.02 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             27.85              28.18 
[1] "0.3 - 180.2 (27.9)" "0.3 - 152.0 (28.2)"
[1] "hr=" "1.4"
D21V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  11P GAIN MUTATED         0    76                0
  11P GAIN WILD-TYPE       2   481                2
D21V3, multiclass
                  clus
vv                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          76                481
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, continuous
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  75
  11P GAIN WILD-TYPE   2 493
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   75
  11P GAIN WILD-TYPE    2  493
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 1                  2
  YES               75                493
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  11P GAIN MUTATED    1  1  1  0
  11P GAIN WILD-TYPE 13 25  4  3
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                1                 13
  R1                1                 25
  R2                1                  4
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     3
  11P GAIN WILD-TYPE                                3    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P GAIN MUTATED                           1
  11P GAIN WILD-TYPE                        31
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           0    70
  11P GAIN WILD-TYPE                                         1   405
D21V7, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                1                 31
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   70                405
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  46
  11P GAIN WILD-TYPE   9 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   46
  11P GAIN WILD-TYPE    9  279
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               46                279
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    52  56
  11Q GAIN WILD-TYPE 214 234
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               108                448 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                56                234 
$`11Q GAIN MUTATED`
TCGA-04-1343 TCGA-04-1346 TCGA-04-1350 TCGA-04-1361 TCGA-04-1516 TCGA-04-1646 
       11.87        65.52        63.98        32.52        41.59        27.88 
TCGA-04-1652 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 
       31.86        35.57         9.99        38.43        61.87        55.36 
TCGA-10-0931 TCGA-13-0726 TCGA-13-0764 TCGA-13-0797 TCGA-13-0885 TCGA-13-0887 
       32.28        31.10        31.04         8.71        91.40        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-1407 TCGA-13-1410 
       70.39        67.99        43.36        57.47         6.05         4.70 
TCGA-13-1412 TCGA-13-1484 TCGA-13-1497 TCGA-13-1499 TCGA-13-1506 TCGA-13-2057 
        5.33        98.04        54.31        38.40         4.41        14.24 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1029 
       16.70         2.66        47.54        42.54        15.39         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1119 
       29.13        18.90         2.24        51.35         3.22       129.96 
TCGA-23-2072 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-1417 TCGA-24-1427 
       24.95        49.84         4.70         4.50         7.82         4.83 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1471 TCGA-24-1548 TCGA-24-1549 
       19.17        18.67         8.55         1.18        16.21        56.58 
TCGA-24-1551 TCGA-24-1556 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 TCGA-24-1604 
       51.91        70.62        19.53        47.70        25.87        88.37 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 TCGA-24-1928 
       38.24         8.32         3.72         3.81         5.52        11.05 
TCGA-24-2027 TCGA-24-2033 TCGA-25-1312 TCGA-25-1322 TCGA-25-1630 TCGA-25-1631 
      109.71        18.48         1.02         2.99         7.86         0.30 
TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 TCGA-25-2400 TCGA-29-1691 TCGA-29-1701 
       51.22        18.05        85.05        42.02        47.18        16.90 
TCGA-29-1702 TCGA-29-1763 TCGA-29-1764 TCGA-29-1774 TCGA-29-1783 TCGA-29-2425 
       18.67        66.81        62.93        17.33         7.23        65.00 
TCGA-29-2429 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 
        4.90        51.91         2.47        15.68         0.26         6.12 
TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 TCGA-36-2551 TCGA-42-2587 TCGA-57-1584 
       22.55        30.08        27.85        16.18        23.74        21.14 
TCGA-59-2351 TCGA-61-1722 TCGA-61-1740 TCGA-61-1906 TCGA-61-1907 TCGA-61-1915 
      116.12         8.09         2.43        34.13        31.30        67.76 
TCGA-61-1918 TCGA-61-2097 TCGA-61-2109 TCGA-61-2612 TCGA-OY-A56P TCGA-VG-A8LO 
       15.75        60.62        20.68         6.35        39.68         0.79 

$`11Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 
       18.51        63.09        48.76        21.57        65.46        49.28 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       44.32        33.67        76.57        71.47        82.39        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       19.99        38.37       119.08        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 
       48.89        28.64        64.64        36.23        47.70        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1662 TCGA-09-1664 
       29.16         9.47        57.76        17.98        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        57.60        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        8.55        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
      112.41        71.11        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        54.31        25.91        81.47        18.51        33.24 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       11.70         3.91        35.44        35.80        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
        6.21        24.59        44.55        39.58         2.73        12.39 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       15.19        17.82        55.17         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.54        34.06        32.25        21.40         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 
       36.72        28.70        30.35        19.59         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        43.86        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0889 TCGA-13-0891 TCGA-13-0899 
       68.94       107.18        74.27        61.84        69.01        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       14.89        13.81         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1477 
        6.61         7.36         5.92         6.84         4.21        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       87.06        61.71        29.42        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 
       37.61        13.97        32.84        16.57         4.21         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.91         3.09        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       10.78         8.75         6.28        54.77         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       25.94        26.20        72.20        27.52        25.38        19.10 
TCGA-20-1686 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1110 
        2.93        40.54        26.83        31.76        49.41        54.51 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 
       31.20        68.68         4.57        33.30        86.01         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
        6.38        39.09        33.47        58.13         0.53       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 TCGA-24-0968 
       87.48        91.66        77.00         2.76         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 
       63.55        47.41         6.31         6.38         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 
        0.76         6.25         6.02         5.95         5.36        17.39 
TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       28.37        43.53        72.92        12.46        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        9.11         3.45        22.22        26.96        57.40        64.27 
TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1560 
       41.06        41.39        58.09        88.50        39.88        44.09 
TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1843 
       45.50        10.26        17.23        90.15        48.33         3.48 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
        4.37        11.28         5.79         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       16.44        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       34.82        14.43        53.95        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86        53.26        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       12.00         2.96        18.58        18.02        15.81         0.36 
TCGA-25-1628 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
       20.61        56.94        60.59        35.54        14.96        24.99 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       45.01        19.99         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        44.71       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       31.20        68.32         0.53        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1766 TCGA-29-1768 
       29.23        34.62        17.00        85.68        39.12        31.23 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       22.98        24.36        22.55        12.36        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
       14.93         8.38         5.36        34.62        86.17        62.47 
TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11        42.25        11.84        11.47         9.76        21.04 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 
       38.07        36.26        48.10        44.91        34.78        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 
        2.20        28.77        29.10        21.53        22.85         8.55 
TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       25.74        24.23        24.69        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.82        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 
       20.98        18.31        20.52        14.17         6.05        11.47 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        7.99        26.04         9.44        42.02         7.46        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
        1.48        24.03        11.38         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 
       25.08        25.02       180.20        80.12        22.32         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 
       34.39         2.14         5.42        44.81        20.52        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       20.94        31.43        18.54        27.88         4.34        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 
       28.47        48.79        44.84        35.80        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        1.45         8.42         5.79        11.41        13.02         9.07 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 
       37.05        42.51        48.92        56.61        43.43        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       39.85        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
        4.77        51.72        71.74        61.64        58.39        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        44.52       125.75        22.22 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56Q TCGA-WR-A838 
       31.07         8.61        18.94         8.05 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.26               0.36 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            129.96             180.20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            23.145             28.735 
[1] "0.3 - 130.0 (23.1)" "0.4 - 180.2 (28.7)"
[1] "hr=" "1"  
D22V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  11Q GAIN MUTATED         0   109                0
  11Q GAIN WILD-TYPE       2   448                2
D22V3, multiclass
                  clus
vv                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                         109                448
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, continuous
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0 112
  11Q GAIN WILD-TYPE   3 456
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0  112
  11Q GAIN WILD-TYPE    3  456
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                  3
  YES              112                456
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  11Q GAIN MUTATED    1  6  2  0
  11Q GAIN WILD-TYPE 13 20  3  3
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                1                 13
  R1                6                 20
  R2                2                  3
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     3
  11Q GAIN WILD-TYPE                                3    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q GAIN MUTATED                           6
  11Q GAIN WILD-TYPE                        26
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           0    97
  11Q GAIN WILD-TYPE                                         1   378
D22V7, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                6                 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   97                378
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  64
  11Q GAIN WILD-TYPE  10 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   64
  11Q GAIN WILD-TYPE   10  261
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               64                261
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   113 129
  12P GAIN WILD-TYPE 153 161
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               242                314 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               129                161 
$`12P GAIN MUTATED`
TCGA-04-1332 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 TCGA-04-1356 
       41.00        18.51        65.52        63.09        65.46        49.28 
TCGA-04-1362 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       44.32        82.39        41.59        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       29.10        84.20        27.88        31.86        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
        9.47        57.76        17.98        35.57         9.99        38.43 
TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2049 
       55.36        17.98         5.85         8.55         6.18       112.41 
TCGA-09-2051 TCGA-09-2053 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       63.09        39.75        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 
       32.28        11.70        19.86        24.59        39.58        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 
       17.82        55.17        11.18        11.54        32.25        31.04 
TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0802 TCGA-13-0883 
       36.72        30.35        19.59         8.12         8.19        68.94 
TCGA-13-0884 TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 
      107.18        70.39        67.99        56.15        19.36        48.33 
TCGA-13-0906 TCGA-13-0912 TCGA-13-0920 TCGA-13-0923 TCGA-13-1407 TCGA-13-1411 
       44.94        34.06        13.81         6.41         6.05         4.21 
TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1489 TCGA-13-1495 TCGA-13-1496 
       87.06        98.04        20.68        82.88        49.25         4.24 
TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-2057 TCGA-13-2059 
       38.40        16.57         4.21         4.41        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-1682 TCGA-20-1686 
        8.61        10.78         8.75         8.42        27.52         2.93 
TCGA-23-1021 TCGA-23-1024 TCGA-23-1030 TCGA-23-1032 TCGA-23-1111 TCGA-23-1114 
       47.54        15.39        29.13         2.24         3.22        68.68 
TCGA-23-1116 TCGA-23-1118 TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 TCGA-23-2643 
        4.57        86.01        58.13         0.53        91.66         4.70 
TCGA-23-2645 TCGA-24-0968 TCGA-24-0982 TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 
        4.50        19.66        22.32         7.99         0.76         6.02 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 
        4.83        28.37        18.67         8.55        12.46        45.14 
TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        9.11        22.22        26.96        57.40        64.27        16.21 
TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 
       58.09        39.88        19.53        44.09        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       10.26        17.23        88.37        48.33        38.24         8.32 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1928 
        3.72         3.81        11.28         5.52         9.80        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 
       81.11         4.87       152.02        18.48        44.52        36.16 
TCGA-24-2261 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 
        0.79        44.61         0.82        67.36        16.64        33.11 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 TCGA-25-1321 TCGA-25-1323 
        1.02        26.96        51.06        34.98        33.96        12.00 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       15.81         0.36         7.86        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 
       24.99        18.05        85.05        13.02         1.02        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-29-1690 TCGA-29-1695 TCGA-29-1698 
        3.02        45.01        42.02        44.71         0.79        68.32 
TCGA-29-1699 TCGA-29-1702 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 
        0.53        18.67        29.23        17.00        66.81        39.12 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 
       31.23        22.98        17.33        12.36        12.30        14.93 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 
        7.23         5.36        86.17        65.00        45.11        42.25 
TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1859 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 
       21.04        15.68        48.10        36.62         1.22        24.26 
TCGA-30-1891 TCGA-31-1950 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 TCGA-36-1571 
       30.05        18.77        42.51         2.20        29.10        22.85 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 TCGA-36-2543 TCGA-36-2547 
        8.55        30.08        24.23        35.05         2.24        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-57-1582 TCGA-57-1583 
       14.17        16.18        11.47        23.74        24.03        11.38 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 
       22.32        25.08        25.02       180.20       116.12         9.40 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        5.42        44.81         8.09        27.88         4.34        31.79 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1904 
        2.43        33.67        43.69         1.45         5.79         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1915 TCGA-61-1917 TCGA-61-2002 TCGA-61-2009 
       34.13        31.30        67.76        43.43        17.98        39.85 
TCGA-61-2012 TCGA-61-2097 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P 
       30.64        60.62       125.75         6.35         8.61        39.68 
TCGA-OY-A56Q TCGA-WR-A838 
       18.94         8.05 

$`12P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       40.24         1.81        49.15         2.01        46.62        11.87 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 
       48.76        21.57        63.98        32.52        33.67        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 
       71.47        56.55        55.43        48.89        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       36.23        47.70        89.33        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
       61.87        30.51         3.02        97.55         6.12        35.15 
TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
        4.54        71.11        20.94        26.93        12.46        54.31 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 
        3.91        35.44        35.80        15.12         6.21        44.55 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 
        2.73        12.39        31.10         2.50        11.38        34.06 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 
       21.40         8.45        38.93        28.70         8.71         7.79 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 
        8.28        43.86        35.28        35.28        13.61        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       74.27        66.67        61.84        69.01        43.36        57.47 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       57.07        47.38        47.84        44.84        37.08        27.72 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 
       29.98        21.17        14.89         4.64         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 
        6.61         7.36         5.92         6.84         4.70         5.33 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 
       54.64        61.71        29.42        22.39        70.82        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
       73.55        38.20        54.31        37.61        13.97        32.84 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2071 
        4.77         4.18         2.56         3.91         3.09         6.28 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 
       54.77        23.05        25.94        26.20        72.20        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
       19.10        16.70         2.66        42.54        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 
       31.76        49.41         8.81        18.90        51.35        54.51 
TCGA-23-1113 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       31.20        33.30       129.96         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 
       33.47        24.95       115.89        87.48        77.00        49.84 
TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        2.76         7.63        11.64        21.80        41.56         7.66 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 
        7.86         6.25         5.95         5.36        17.39        19.17 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1549 
       43.53        72.92       105.99         3.45         1.18        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1562 
       41.06        51.91        41.39        88.50        70.62        45.50 
TCGA-24-1603 TCGA-24-1843 TCGA-24-1846 TCGA-24-1849 TCGA-24-1923 TCGA-24-1924 
       90.15         3.48         4.37         5.79        22.68        30.21 
TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
       16.44        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 
       53.95        28.18        64.01        57.07         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 
       31.63        70.45        36.23        55.86        53.26        32.02 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 
       37.02         1.02        65.00        36.95         2.99         2.96 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       18.58        18.02        20.61         0.30        56.94        60.59 
TCGA-25-2391 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       49.05        12.00        19.99         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       26.99        78.90        47.18       101.79        38.53        33.70 
TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
       31.20        16.90        59.67        18.25        41.98        34.62 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1770 TCGA-29-1771 TCGA-29-1776 TCGA-29-1781 
       85.68        62.93        24.36        22.55        11.84         8.38 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       34.62        62.47         4.90        11.84        11.47         9.76 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 TCGA-30-1860 
       38.07        51.91        36.26         2.47         0.26        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       34.78         6.12        57.57        48.79        45.57        30.18 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 
       22.49         6.71        44.12        28.77        21.53        22.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       25.74        27.85        24.69        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 
       25.91        25.08        23.80        21.60        20.98        18.31 
TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
        6.05         7.99        26.04         9.44        42.02         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-59-2349 
       40.77         1.48        21.14         1.74        29.00        80.12 
TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 
       22.32        34.39         2.14        20.52        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       31.43        18.54        28.47        48.79        44.84        35.80 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
        8.42        11.41        13.02        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       56.61        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
        4.01        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
        4.77        51.72        71.74        61.64        58.39        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 
       55.50         6.48        76.87        20.68        44.52        22.22 
TCGA-61-2613 TCGA-VG-A8LO 
       31.07         0.79 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.36               0.26 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            180.20             129.96 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            24.245             30.195 
[1] "0.4 - 180.2 (24.2)" "0.3 - 130.0 (30.2)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  12P GAIN MUTATED         1   243                2
  12P GAIN WILD-TYPE       1   314                0
D23V3, multiclass
                  clus
vv                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         243                314
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V4, continuous
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     1 252
  12P GAIN WILD-TYPE   2 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1  252
  12P GAIN WILD-TYPE    2  316
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 1                  2
  YES              252                316
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED    7 11  2  1
  12P GAIN WILD-TYPE  7 15  3  2
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0                7                  7
  R1               11                 15
  R2                2                  3
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  1     5
  12P GAIN WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P GAIN MUTATED                          15
  12P GAIN WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           1   208
  12P GAIN WILD-TYPE                                         0   267
D23V7, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    5                 13
  BLACK OR AFRICAN AMERICAN                               15                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  208                267
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     2 128
  12P GAIN WILD-TYPE   8 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2  128
  12P GAIN WILD-TYPE    8  197
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO              128                197
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    73  93
  12Q GAIN WILD-TYPE 193 197
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               166                390 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                93                197 
$`12Q GAIN MUTATED`
TCGA-04-1332 TCGA-04-1337 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1362 
       41.00         2.01        18.51        65.52        63.09        44.32 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 
       38.37       119.08        29.10        27.88        31.86        45.37 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1668 TCGA-09-1670 
        9.47        57.76        17.98        35.57        55.36        17.98 
TCGA-09-1672 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 TCGA-10-0926 TCGA-10-0927 
        5.85         4.54       112.41        39.75        25.91        81.47 
TCGA-10-0930 TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 TCGA-13-0762 
       33.24        35.80        24.59        39.58        15.19        32.25 
TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0883 TCGA-13-0884 TCGA-13-0888 
       19.59         8.12        35.28        68.94       107.18        70.39 
TCGA-13-0890 TCGA-13-0912 TCGA-13-0920 TCGA-13-1407 TCGA-13-1481 TCGA-13-1484 
       67.99        34.06        13.81         6.05        87.06        98.04 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1496 TCGA-13-1499 TCGA-13-1505 TCGA-13-1506 
       20.68        70.82         4.24        38.40         4.21         4.41 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-20-1682 TCGA-20-1685 
       14.24         8.61        10.78         8.75        27.52        16.70 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1032 TCGA-23-1111 TCGA-23-1116 TCGA-23-1809 
        2.93        47.54         2.24         3.22         4.57         0.53 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-1418 TCGA-24-1419 TCGA-24-1424 
        4.70         4.50        19.66         7.99         7.86         6.02 
TCGA-24-1434 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 
       18.67        12.46        45.14         9.11        22.22        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 
       57.40        16.21        39.88        19.53        44.09        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 
       25.87        10.26        38.24         3.72         3.81        11.28 
TCGA-24-1850 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2033 
        5.52        11.05        81.11         4.87       152.02        18.48 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2281 TCGA-24-2288 TCGA-24-2293 
       44.52        36.16         0.79        44.61         0.82        16.64 
TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 TCGA-25-1321 
       33.11         1.02        26.96        51.06        34.98        33.96 
TCGA-25-1323 TCGA-25-1627 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       12.00         0.36        35.54        51.22        14.96        24.99 
TCGA-25-2392 TCGA-25-2398 TCGA-29-1690 TCGA-29-1695 TCGA-29-1698 TCGA-29-1710 
        1.02        45.01        44.71         0.79        68.32        29.23 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1774 TCGA-29-1778 
       17.00        66.81        39.12        31.23        17.33        14.93 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 
        7.23         5.36        86.17        65.00        45.11        42.25 
TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1859 TCGA-30-1866 TCGA-30-1867 TCGA-31-1950 
       21.04        15.68        48.10        36.62         1.22        18.77 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1571 TCGA-36-1575 TCGA-36-2529 TCGA-36-2543 
       42.51         2.20        22.85         8.55        35.05         2.24 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-57-1583 
       20.52        14.17        16.18        11.47        23.74        11.38 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 
       22.32        25.08        25.02       180.20       116.12         9.40 
TCGA-59-2372 TCGA-61-1730 TCGA-61-1733 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       44.81         4.34        31.79         2.43        33.67        43.69 
TCGA-61-1906 TCGA-61-1907 TCGA-61-2009 TCGA-61-2012 TCGA-61-2088 TCGA-61-2097 
       34.13        31.30        39.85        30.64         4.77        60.62 
TCGA-61-2102 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 
        6.48       125.75         6.35         8.61 

$`12Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 TCGA-04-1348 
       40.24         1.81        49.15        46.62        11.87        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 
       21.57        63.98        65.46        49.28        32.52        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       76.57        71.47        82.39        56.55        41.59        19.99 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       84.20        55.43        48.89        28.64        64.64        36.23 
TCGA-04-1654 TCGA-09-0364 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       47.70        29.16         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1673 TCGA-09-1674 
       41.62        57.60        61.87        30.51         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2050 TCGA-09-2051 
       97.55         6.18         6.12        35.15        71.11        63.09 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0928 TCGA-10-0931 
       20.94        26.93        12.46        54.31        18.51        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       11.70         3.91        35.44        15.12        19.86         6.21 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 
       44.55         2.73        12.39        31.10        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 
        2.50        11.18        11.38        11.54        34.06        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 
        8.71         7.79         8.28         8.19        43.86        35.28 
TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
       13.61        91.40        74.27        66.67        61.84        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       48.33        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        14.89         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       10.88         6.61         7.36         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 
        4.21         5.33        54.64        61.71        29.42        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 
       82.88        52.44        73.55        38.20        49.25        54.31 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1507 TCGA-13-1509 
       37.61        13.97        32.84        16.57         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2071 TCGA-13-A5FT 
        2.56         3.91         3.09        12.23         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 
        8.42        23.05        25.94        26.20        72.20        25.38 
TCGA-20-1684 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       19.10         2.66        42.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 
       31.76        49.41         8.81        29.13        18.90        51.35 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       54.51        31.20        68.68        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
        4.27         6.38        39.09        33.47        58.13        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        7.63        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        0.76         6.25         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1467 
       28.37        19.17        43.53         8.55        72.92       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
        3.45         1.18        64.27        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1562 TCGA-24-1567 
       41.39        58.09        88.50        70.62        45.50        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 
       90.15        88.37        48.33         8.32         3.48         4.37 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-2023 
        5.79         9.80        22.68        30.21        16.44        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 
       58.16        34.82       109.71        14.43        53.95        28.18 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       64.01        57.07         0.36        47.54        31.63        70.45 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 TCGA-25-1316 
       67.36        36.23        55.86        53.26        32.02        37.02 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
        1.02        65.00        36.95         2.99         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       18.02        15.81        20.61         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 
       60.59        18.05        85.05        13.02        49.05        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
        3.02        12.00        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       31.00        26.99        78.90        47.18       101.79        38.53 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.70        31.20         0.53        16.90        18.67        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1769 
       18.25        41.98        34.62        85.68        62.93        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       24.36        22.55        12.36        11.84        12.30         8.38 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       34.62        62.47         4.90        11.84        11.47         9.76 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 TCGA-30-1860 
       38.07        51.91        36.26         2.47         0.26        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       34.78         6.12        57.57        24.26        30.05        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 
       45.57        30.18        22.49         6.71        44.12        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       29.10        21.53        22.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.23        24.69        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 
       25.08        23.80        21.60        20.98        18.31         6.05 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        7.99        26.04         9.44        42.02         7.46        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-59-2349 
        1.48        24.03        21.14         1.74        29.00        80.12 
TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1721 
       22.32        34.39         2.14         5.42        20.52        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 
        8.09        20.94        31.43        18.54        27.88        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       48.79        44.84        35.80         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       11.41        13.02         9.07        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       56.61        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 
        5.52        14.50        17.98         4.01        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96        45.40         4.80        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       58.39        65.52        55.50        76.87        20.68        44.52 
TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       22.22        31.07        39.68        18.94         0.79         8.05 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.36               0.26 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            180.20             129.96 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            24.790             29.115 
[1] "0.4 - 180.2 (24.8)" "0.3 - 130.0 (29.1)"
[1] "hr=" "1.2"
D24V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  12Q GAIN MUTATED         1   166                2
  12Q GAIN WILD-TYPE       1   391                0
D24V3, multiclass
                  clus
vv                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         166                391
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V4, continuous
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1 174
  12Q GAIN WILD-TYPE   2 394
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1  174
  12Q GAIN WILD-TYPE    2  394
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                  2
  YES              174                394
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  12Q GAIN MUTATED    5 11  0  0
  12Q GAIN WILD-TYPE  9 15  5  3
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0                5                  9
  R1               11                 15
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     2
  12Q GAIN WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q GAIN MUTATED                          10
  12Q GAIN WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           1   144
  12Q GAIN WILD-TYPE                                         0   331
D24V7, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                               10                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  144                331
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1  84
  12Q GAIN WILD-TYPE   9 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   84
  12Q GAIN WILD-TYPE    9  241
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               84                241
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    25  32
  13Q GAIN WILD-TYPE 241 258
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                57                499 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                32                258 
$`13Q GAIN MUTATED`
TCGA-04-1337 TCGA-04-1351 TCGA-04-1371 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 
        2.01        65.46        82.39        29.16         9.47        35.57 
TCGA-09-2049 TCGA-10-0933 TCGA-10-0935 TCGA-13-0727 TCGA-13-0757 TCGA-13-0899 
      112.41        11.70        35.44        15.19        11.18        56.15 
TCGA-13-0921 TCGA-13-1407 TCGA-13-1408 TCGA-13-1481 TCGA-13-1484 TCGA-13-1506 
        4.64         6.05         5.92        87.06        98.04         4.41 
TCGA-23-1030 TCGA-23-1109 TCGA-23-2072 TCGA-24-0970 TCGA-24-1418 TCGA-24-1422 
       29.13        51.35        24.95        11.64         7.99         0.76 
TCGA-24-1434 TCGA-24-1467 TCGA-24-1471 TCGA-24-1930 TCGA-25-1312 TCGA-25-1317 
       18.67       105.99         1.18        81.11         1.02         1.02 
TCGA-25-1320 TCGA-25-1323 TCGA-25-1626 TCGA-25-1870 TCGA-25-2398 TCGA-29-1695 
       36.95        12.00        15.81        14.96        45.01         0.79 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1770 TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 
       29.23        17.00        24.36         7.23        65.00        45.11 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1880 TCGA-36-1576 TCGA-36-2552 
       38.07        51.91        36.26        57.57        30.08        11.47 
TCGA-42-2591 TCGA-57-1993 TCGA-59-2355 TCGA-61-1911 TCGA-61-2003 TCGA-61-2008 
       40.77        25.08         2.14        42.51         4.01        30.64 
TCGA-61-2009 TCGA-61-2098 TCGA-61-2102 
       39.85        65.52         6.48 

$`13Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00         1.81        49.15        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       56.55        41.59        19.99        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       84.20        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-0367 
       36.23        31.86        47.70        45.37        57.76        17.98 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
        9.99        38.43        89.33        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       61.87        55.36        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        8.55        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       54.31        25.91        81.47        18.51        33.24        32.28 
TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        3.91        35.80        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 
       44.55        39.58         2.73        12.39        31.10        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       55.17         2.50        11.38        11.54        34.06        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       30.35        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.19        43.86        35.28        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
      107.18        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 
       67.99        69.01        43.36        57.47        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 
        6.41         6.08        10.88         6.61         7.36         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 
        4.70         4.21         5.33        54.64        61.71        29.42 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       20.68        22.39        70.82        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       38.20        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 
       13.97        32.84        16.57         4.21         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        2.56         3.91         3.09        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       10.78         8.75         6.28        54.77         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       25.94        26.20        72.20        27.52        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       16.70         2.93         2.66        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 
       15.39        26.83        31.76        49.41         8.81        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        2.24        54.51         3.22        31.20        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       33.30        86.01       129.96         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13         0.53       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       19.66        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 
       63.55        47.41         6.31         6.38         7.82         7.86 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       28.37        19.17        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       45.14         9.11         3.45        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       88.37        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.81         4.37        11.28         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 
       22.68        30.21        16.44        11.05         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
        0.82        67.36        36.23        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 
       53.26        26.96        32.02        51.06        37.02        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       65.00        33.96         2.99         2.96        18.58        18.02 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
        0.36        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       35.54        51.22        24.99        18.05        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 
       49.05         1.02        38.04         3.02        12.00        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       42.02         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 
       44.71        47.18       101.79        38.53        33.70        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32         0.53        16.90        18.67        59.67        18.25 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       41.98        34.62        85.68        66.81        62.93        39.12 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       31.23        22.98        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       12.30        14.93         8.38         5.36        34.62        86.17 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       62.47         4.90        42.25        11.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       21.04         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 
       34.78         6.12        36.62         1.22        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       42.51        44.12         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.85        22.55         8.55        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.69        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 
       20.52        14.17         6.05        16.18         7.99        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 
       23.74         9.44        42.02         7.46         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 
       11.38        21.14         1.74        22.32        29.00        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
      180.20        80.12        22.32       116.12         9.40        34.39 
TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
        5.42        44.81        20.52        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       31.43        18.54        27.88         4.34        31.79        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       48.79        44.84        35.80         2.43        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
        1.45         8.42         5.79        11.41        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       34.13        31.30        37.05        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       43.43        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       17.98        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.77        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50        76.87        20.68        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-WR-A838 
        8.05 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.76               0.26 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            112.41             180.20 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             25.08              28.18 
[1] "0.8 - 112.4 (25.1)" "0.3 - 180.2 (28.2)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  13Q GAIN MUTATED         0    57                0
  13Q GAIN WILD-TYPE       2   500                2
D25V3, multiclass
                  clus
vv                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          57                500
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, continuous
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1  58
  13Q GAIN WILD-TYPE   2 510
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   58
  13Q GAIN WILD-TYPE    2  510
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 1                  2
  YES               58                510
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN MUTATED    2  2  0  0
  13Q GAIN WILD-TYPE 12 24  5  3
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                2                 12
  R1                2                 24
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     2
  13Q GAIN WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q GAIN MUTATED                           1
  13Q GAIN WILD-TYPE                        31
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           0    52
  13Q GAIN WILD-TYPE                                         1   423
D25V7, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                1                 31
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   52                423
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  38
  13Q GAIN WILD-TYPE  10 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   38
  13Q GAIN WILD-TYPE   10  287
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               38                287
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    28  29
  14Q GAIN WILD-TYPE 238 261
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                57                499 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                29                261 
$`14Q GAIN MUTATED`
TCGA-04-1514 TCGA-04-1517 TCGA-04-1646 TCGA-04-1652 TCGA-09-0364 TCGA-09-1668 
       56.55        19.99        27.88        31.86        29.16        55.36 
TCGA-09-1669 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 TCGA-13-0899 TCGA-13-0901 
       30.51        32.25         8.45        19.59        56.15        19.36 
TCGA-13-1408 TCGA-13-1501 TCGA-13-1505 TCGA-13-2057 TCGA-13-2059 TCGA-20-0991 
        5.92        32.84         4.21        14.24        12.23        26.20 
TCGA-23-1116 TCGA-23-1809 TCGA-24-1103 TCGA-24-1417 TCGA-24-1422 TCGA-24-1545 
        4.57         0.53        54.12         7.82         0.76        57.40 
TCGA-24-1555 TCGA-24-1842 TCGA-24-1844 TCGA-24-1923 TCGA-24-2030 TCGA-24-2261 
       88.50         8.32         3.72        22.68        53.95         0.79 
TCGA-25-1314 TCGA-25-1317 TCGA-25-1321 TCGA-25-1628 TCGA-25-1878 TCGA-25-2401 
       32.02         1.02        33.96        20.61        85.05         2.96 
TCGA-25-2408 TCGA-29-1701 TCGA-29-1702 TCGA-29-1784 TCGA-29-2428 TCGA-30-1714 
       31.00        16.90        18.67         5.36        45.11        38.07 
TCGA-30-1853 TCGA-30-1866 TCGA-31-1959 TCGA-36-1570 TCGA-36-2544 TCGA-36-2545 
       36.26        36.62         2.20        21.53        20.98        18.31 
TCGA-36-2548 TCGA-57-1583 TCGA-59-2352 TCGA-59-2355 TCGA-61-1730 TCGA-61-2012 
       14.17        11.38         9.40         2.14         4.34        30.64 
TCGA-61-2097 TCGA-61-2612 TCGA-WR-A838 
       60.62         6.35         8.05 

$`14Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       63.98        65.46        49.28        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 
       76.57        71.47        82.39        41.59        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 
       29.10        84.20        55.43        48.89        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       36.23        47.70        45.37         9.47        57.76        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       35.57         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       57.60        61.87        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       97.55         6.18         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       54.31        25.91        81.47        18.51        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       11.70         3.91        35.44        35.80        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
        6.21        24.59        44.55        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.10        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 
       11.38        11.54        34.06        31.04        21.40        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       36.72        28.70        30.35         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        43.86        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       68.94       107.18        91.40        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 
       61.84        67.99        69.01        43.36        57.47        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        6.05         6.84         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       87.06        61.71        29.42        98.04        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 
        4.24        54.31        37.61        38.40        13.97        16.57 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.41         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        8.61        10.78         8.75         6.28        54.77         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       23.05        25.94        72.20        27.52        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       16.70         2.93         2.66        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       18.90         2.24        51.35        54.51         3.22        31.20 
TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       68.68        33.30        86.01       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       39.09        33.47        58.13        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       91.66        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 
       22.32        63.55        47.41         6.31         6.38         7.99 
TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        7.86         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        19.17        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       72.92        12.46        45.14       105.99         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
        1.18        22.22        26.96        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 
       41.06        51.91        41.39        58.09        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 
       17.23        90.15        88.37        48.33        38.24         3.48 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.81         4.37        11.28         5.79         5.52         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       30.21        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 
       44.84        58.16        34.82       109.71        14.43        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 
       28.18        64.01        44.52        57.07        36.16         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       47.54        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
       36.23        16.64        33.11        55.86        53.26         1.02 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       26.96        51.06        37.02        34.98        65.00        36.95 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
        2.99        12.00         2.96        18.58        18.02        15.81 
TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
        0.36         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 
       51.22        14.96        24.99        18.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
        1.02        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
       42.02        29.03        26.99        78.90        44.71        47.18 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
        0.53        59.67        18.25        41.98        29.23        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       17.00        85.68        66.81        62.93        39.12        31.23 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 
       12.30        14.93         8.38         7.23        34.62        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       65.00        62.47         4.90        42.25        11.84        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
        9.76        21.04        51.91         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 
       48.10        44.91        34.78         6.12         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 
       22.49         6.71        42.51        44.12        28.77        29.10 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       24.23        24.69        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2547 
       25.91        25.08        23.80        21.60         2.24        20.52 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
        6.05        16.18        11.47         7.99        26.04        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
        9.44        42.02         7.46        40.77         1.48        24.03 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       21.14         1.74        22.32        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2363 
      180.20        80.12        22.32       116.12        34.39         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       44.81        20.52        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       18.54        27.88        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       35.80         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        4.01        30.64        39.85         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75        22.22        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO 
        0.79 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.53               0.26 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              88.5              180.2 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             19.99              29.00 
[1] "0.5 - 88.5 (20.0)"  "0.3 - 180.2 (29.0)"
[1] "hr=" "1.4"
D26V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  14Q GAIN MUTATED         0    58                0
  14Q GAIN WILD-TYPE       2   499                2
D26V3, multiclass
                  clus
vv                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          58                499
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, continuous
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2  56
  14Q GAIN WILD-TYPE   1 512
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   56
  14Q GAIN WILD-TYPE    1  512
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 2                  1
  YES               56                512
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  14Q GAIN MUTATED    1  4  0  0
  14Q GAIN WILD-TYPE 13 22  5  3
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                1                 13
  R1                4                 22
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     1
  14Q GAIN WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q GAIN MUTATED                           4
  14Q GAIN WILD-TYPE                        28
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           0    49
  14Q GAIN WILD-TYPE                                         1   426
D26V7, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    1                 17
  BLACK OR AFRICAN AMERICAN                                4                 28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   49                426
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  31
  14Q GAIN WILD-TYPE  10 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   31
  14Q GAIN WILD-TYPE   10  294
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               31                294
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    24  13
  15Q GAIN WILD-TYPE 242 277
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                37                519 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                13                277 
$`15Q GAIN MUTATED`
TCGA-04-1349 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-09-0369 TCGA-09-1675 
       21.57        65.46        32.52        44.32        35.57        97.55 
TCGA-09-2053 TCGA-10-0938 TCGA-13-0761 TCGA-13-0792 TCGA-13-0890 TCGA-13-0919 
       39.75        19.86        34.06        36.72        67.99        14.89 
TCGA-13-1412 TCGA-13-1499 TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 TCGA-23-1021 
        5.33        38.40        12.23         8.75         6.28        47.54 
TCGA-23-2072 TCGA-23-2079 TCGA-24-1413 TCGA-24-1419 TCGA-24-1551 TCGA-24-1558 
       24.95        91.66         6.31         7.86        51.91        19.53 
TCGA-25-1627 TCGA-30-1853 TCGA-31-1959 TCGA-36-1571 TCGA-36-2542 TCGA-57-1582 
        0.36        36.26         2.20        22.85        21.60        24.03 
TCGA-57-1994 TCGA-61-1730 TCGA-61-1907 TCGA-61-1915 TCGA-61-2009 TCGA-61-2097 
       25.02         4.34        31.30        67.76        39.85        60.62 
TCGA-WR-A838 
        8.05 

$`15Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 
       18.51        11.87        65.52        63.09        48.76        63.98 
TCGA-04-1356 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       49.28        33.67        76.57        71.47        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       41.59        19.99        38.37       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       31.86        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       17.98         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       57.60        61.87        55.36        30.51        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        3.02         8.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
      112.41        71.11        63.09        20.94        26.93        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       54.31        25.91        81.47        18.51        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 
       11.70         3.91        35.44        35.80        15.12         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       24.59        44.55        39.58         2.73        12.39        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       15.19        17.82        55.17         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.54        32.25        31.04        21.40         8.45        38.93 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       28.70        30.35        19.59         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        43.86        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       68.94       107.18        91.40        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       61.84        69.01        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36        47.38        48.33        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       37.08        27.72        34.06        29.98        21.17        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 
        6.05         5.92         6.84         4.70         4.21        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       87.06        61.71        29.42        98.04        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.21         4.41         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU 
        3.09        14.24         8.61        10.78        54.77         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       23.05        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 
       19.10        16.70         2.93         2.66        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       18.90         2.24        51.35        54.51         3.22        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       68.68         4.57        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
        6.38        39.09        33.47        58.13         0.53       115.89 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       87.48        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 
       22.32        54.12        63.55        47.41         6.38         7.82 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.99         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        4.83        17.39        28.37        19.17        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
        8.55        72.92        12.46        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        3.45         1.18        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        41.06        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       70.62        39.88        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       10.26        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
        8.32         3.48         3.72         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        5.79         5.52         9.80        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       11.05        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       34.82       109.71        14.43        53.95        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 
       64.01        44.52        57.07        36.16         0.79         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       47.54        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
       36.23        16.64        33.11        55.86        53.26         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        32.02        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       65.00        36.95        33.96         2.99        12.00         2.96 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.58        18.02        15.81        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       56.94        60.59        35.54        51.22        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       18.05        85.05        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
        3.02        12.00        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
       29.03        31.00        26.99        78.90        44.71        47.18 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
        0.53        16.90        18.67        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       29.23        34.62        17.00        85.68        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.12        31.23        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       12.36        11.84        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        5.36        34.62        86.17        65.00        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
        4.90        42.25        11.84        11.47         9.76        21.04 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       38.07        51.91         2.47        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       44.91        34.78         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 
       22.49         6.71        42.51        44.12        28.77        29.10 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       21.53        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       24.23        24.69        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.91        25.08        23.80         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       20.52        14.17         6.05        16.18        11.47         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       26.04        23.74         9.44        42.02         7.46        40.77 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
        1.48        11.38        21.14         1.74        22.32        29.00 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 
       34.39         2.14         5.42        44.81        20.52        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 
        8.09        20.94        31.43        18.54        27.88        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       28.47        48.79        44.84        35.80         2.43        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       43.69         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
        9.07        34.13        37.05        42.51        48.92        56.61 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       43.43        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       17.98         4.01        30.64        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       58.39        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       39.68        18.94         0.79 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.36               0.26 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             97.55             180.20 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             25.02              28.18 
[1] "0.4 - 97.5 (25.0)"  "0.3 - 180.2 (28.2)"
[1] "hr=" "1.5"
D27V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  15Q GAIN MUTATED         0    38                0
  15Q GAIN WILD-TYPE       2   519                2
D27V3, multiclass
                  clus
vv                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          38                519
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, continuous
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  39
  15Q GAIN WILD-TYPE   3 529
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   39
  15Q GAIN WILD-TYPE    3  529
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                  3
  YES               39                529
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  15Q GAIN MUTATED    0  1  0  0
  15Q GAIN WILD-TYPE 14 25  5  3
D27V6, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 47 
        TCGA-04-1516         TCGA-04-1644         TCGA-13-0807 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-13-0911         TCGA-13-A5FT         TCGA-13-A5FU 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-24-2033         TCGA-29-2414         TCGA-29-2425 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-29-2427         TCGA-29-2428         TCGA-29-2429 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-29-2431         TCGA-29-2432         TCGA-29-2434 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-29-2436         TCGA-36-2529         TCGA-36-2530 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-36-2532         TCGA-36-2534         TCGA-36-2537 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-36-2538         TCGA-36-2540         TCGA-36-2543 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-36-2544         TCGA-36-2545         TCGA-36-2547 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-36-2548         TCGA-36-2549         TCGA-36-2551 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-36-2552         TCGA-3P-A9WA         TCGA-42-2582 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-42-2587         TCGA-42-2588         TCGA-42-2589 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-42-2590         TCGA-42-2593         TCGA-57-1993 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-59-2363         TCGA-59-2372         TCGA-61-2612 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-61-2613         TCGA-61-2614         TCGA-OY-A56P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-OY-A56Q         TCGA-VG-A8LO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     1
  15Q GAIN WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q GAIN MUTATED                           2
  15Q GAIN WILD-TYPE                        30
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           0    33
  15Q GAIN WILD-TYPE                                         1   442
D27V7, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    1                 17
  BLACK OR AFRICAN AMERICAN                                2                 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   33                442
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  23
  15Q GAIN WILD-TYPE  10 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   23
  15Q GAIN WILD-TYPE   10  302
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               23                302
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    27  30
  16P GAIN WILD-TYPE 239 260
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                57                499 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                30                260 
$`16P GAIN MUTATED`
TCGA-04-1351 TCGA-04-1371 TCGA-04-1525 TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 
       65.46        82.39        38.37        84.20        27.88        28.64 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-09-1672 TCGA-09-2051 
       45.37        29.16         9.47        35.57         5.85        63.09 
TCGA-10-0936 TCGA-13-0724 TCGA-13-0889 TCGA-13-0897 TCGA-13-0901 TCGA-13-0921 
       35.80         2.73        61.84        57.47        19.36         4.64 
TCGA-13-1487 TCGA-13-1510 TCGA-13-2059 TCGA-20-1682 TCGA-23-1021 TCGA-23-1124 
       22.39         2.56        12.23        27.52        47.54        58.13 
TCGA-23-1809 TCGA-23-2643 TCGA-24-0966 TCGA-24-1434 TCGA-24-1464 TCGA-24-1565 
        0.53         4.70         7.63        18.67        12.46        10.26 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-25-1321 
       88.37        48.33        38.24         8.32         3.81        33.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-29-1691 TCGA-29-1774 TCGA-29-1784 
       24.99        18.05        85.05        47.18        17.33         5.36 
TCGA-29-2432 TCGA-36-1581 TCGA-36-2547 TCGA-36-2552 TCGA-59-2372 TCGA-61-1733 
       11.84        24.69        20.52        11.47        44.81        31.79 
TCGA-61-1738 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 TCGA-61-2009 
       35.80        67.76        43.43        15.75        14.50        39.85 
TCGA-61-2101 TCGA-61-2111 TCGA-OY-A56Q 
       55.50       125.75        18.94 

$`16P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       63.98        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 
       71.47        56.55        41.59        19.99       119.08        29.10 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       55.43        48.89        64.64        36.23        31.86        47.70 
TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       57.76        17.98         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       41.62        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        3.02         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        4.54       112.41        71.11        39.75        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        54.31        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 
        6.21        24.59        44.55        39.58        12.39        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       15.19        17.82        55.17         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.54        34.06        32.25        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       38.93        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        7.79         8.12         8.28         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 
       66.67        70.39        67.99        69.01        43.36        56.15 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       57.07        47.38        48.33        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       37.08        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       54.64        87.06        61.71        29.42        98.04        20.68 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
        4.24        54.31        37.61        38.40        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 
       16.57         4.21         4.41         4.77         4.18         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
        3.09        14.24         8.61        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       54.77         8.42        23.05        25.94        26.20        72.20 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
       25.38        19.10        16.70         2.93         2.66        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        31.76        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.24        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       31.20        68.68         4.57        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 
        4.27         6.38        39.09        33.47        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 
       87.48        91.66        77.00        49.84         2.76         4.50 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        5.36         4.83        17.39        28.37        19.17        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
        8.55        72.92        45.14       105.99         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        1.18        22.22        26.96        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       56.58        41.06        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       70.62        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 
       25.87        17.23        90.15         3.48         3.72         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
       11.28         5.79         5.52         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       16.44        11.05        81.11         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       58.16        34.82       109.71        14.43        53.95        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       28.18        64.01        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       67.36        36.23        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        32.02        51.06        37.02         1.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       34.98        65.00        36.95         2.99        12.00         2.96 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       18.58        18.02        15.81         0.36        20.61         7.86 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        56.94        60.59        35.54        51.22        14.96 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       26.99        78.90        44.71       101.79        38.53         0.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       33.70        31.20        68.32         0.53        16.90        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       59.67        18.25        41.98        29.23        34.62        17.00 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
       85.68        66.81        62.93        39.12        31.23        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       24.36        22.55        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        8.38         7.23        34.62        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11         4.90        42.25        11.47         9.76        21.04 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       38.07        51.91        36.26         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       48.10        44.91        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       18.77        22.49         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       28.77        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 
       30.08        25.74        27.85        24.23        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
        2.24        20.98        18.31        14.17         6.05        16.18 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
        7.99        26.04        23.74         9.44        42.02         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       40.77         1.48        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       20.52        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 
       27.88         4.34        28.47        48.79        44.84         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       33.67        43.69         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       13.02         9.07        34.13        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 
       48.92        56.61        38.17         2.01         5.52        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        4.01        30.64        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        65.52         6.48        76.87        20.68        44.52 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO 
       22.22         6.35        31.07         8.61        39.68         0.79 
TCGA-WR-A838 
        8.05 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.53               0.26 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            125.75             180.20 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             27.88              28.18 
[1] "0.5 - 125.8 (27.9)" "0.3 - 180.2 (28.2)"
[1] "hr=" "1"  
D28V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  16P GAIN MUTATED         0    59                0
  16P GAIN WILD-TYPE       2   498                2
D28V3, multiclass
                  clus
vv                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          59                498
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, continuous
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     0  59
  16P GAIN WILD-TYPE   3 509
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      0   59
  16P GAIN WILD-TYPE    3  509
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 0                  3
  YES               59                509
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  16P GAIN MUTATED    3  1  0  1
  16P GAIN WILD-TYPE 11 25  5  2
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0                3                 11
  R1                1                 25
  R2                0                  5
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     1
  16P GAIN WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P GAIN MUTATED                           4
  16P GAIN WILD-TYPE                        28
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           0    50
  16P GAIN WILD-TYPE                                         1   425
D28V7, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    1                 17
  BLACK OR AFRICAN AMERICAN                                4                 28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   50                425
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  33
  16P GAIN WILD-TYPE   9 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   33
  16P GAIN WILD-TYPE    9  292
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               33                292
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    14  15
  16Q GAIN WILD-TYPE 252 275
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                29                527 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                15                275 
$`16Q GAIN MUTATED`
TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-09-0364 TCGA-09-0369 TCGA-09-1672 
       84.20        27.88        28.64        29.16        35.57         5.85 
TCGA-13-0897 TCGA-13-0921 TCGA-13-1510 TCGA-13-2059 TCGA-23-1021 TCGA-24-1464 
       57.47         4.64         2.56        12.23        47.54        12.46 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1845 TCGA-25-1321 TCGA-29-1774 
       88.37        48.33        38.24         3.81        33.96        17.33 
TCGA-36-1581 TCGA-36-2538 TCGA-36-2547 TCGA-59-2351 TCGA-59-2372 TCGA-61-1738 
       24.69        25.08        20.52       116.12        44.81        35.80 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 TCGA-OY-A56Q 
       67.76        43.43        15.75        14.50        18.94 

$`16Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       63.98        65.46        49.28        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       76.57        71.47        82.39        56.55        41.59        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 
       38.37       119.08        29.10        55.43        48.89        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 TCGA-09-0366 
       36.23        31.86        47.70        45.37         9.47        57.76 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       17.98         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 
       57.60        61.87        55.36        30.51        17.98         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        8.55        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
      112.41        71.11        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        54.31        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       32.28        11.70         3.91        35.44        35.80        15.12 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       19.86         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
       12.39        31.10        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       11.18        11.38        11.54        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       19.59         8.71         7.79         8.12         8.28         8.19 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.28        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       91.40        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       69.01        43.36        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       48.33        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       34.06        29.98        21.17        14.89        13.81         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.08        10.88         6.61         7.36         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       61.71        29.42        98.04        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       54.31        37.61        38.40        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 
        4.21         4.41         4.77         4.18         3.91         3.09 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       14.24         8.61        10.78         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.42        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
       25.38        19.10        16.70         2.93         2.66        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        31.76        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.24        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       31.20        68.68         4.57        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
        4.27         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       24.95       115.89        87.48        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
        2.76         4.70         4.50         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        19.17        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        45.14       105.99         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       10.26        17.23        90.15         8.32         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       30.21        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
        0.82        67.36        36.23        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       53.26         1.02        26.96        32.02        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
        1.02        34.98        65.00        36.95         2.99        12.00 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.96        18.58        18.02        15.81         0.36        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
        7.86         0.30        56.94        60.59        35.54        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       14.96        24.99        18.05        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
        1.02        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       42.02         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       44.71        47.18       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       31.20        68.32         0.53        16.90        18.67        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        29.23        34.62        17.00        85.68 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       66.81        62.93        39.12        31.23        22.98        24.36 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       22.55        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        7.23         5.36        34.62        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       45.11         4.90        42.25        11.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       21.04        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 
        0.26        48.10        44.91        34.78         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 
        8.55        30.08        25.74        27.85        24.23        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 
       33.01        29.49        29.82        25.91        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
        2.24        20.98        18.31        14.17         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       11.47         7.99        26.04        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
        7.46        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.74        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       80.12        22.32         9.40        34.39         2.14         5.42 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       20.52        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
        2.43        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       42.51        48.92        56.61        38.17         2.01         5.52 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       17.98         4.01        30.64        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
       61.64        58.39        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       76.87        20.68        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61        39.68         0.79         8.05 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              2.56               0.26 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            116.12             180.20 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             28.64              27.88 
[1] "2.6 - 116.1 (28.6)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1.1"
D29V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  16Q GAIN MUTATED         0    31                0
  16Q GAIN WILD-TYPE       2   526                2
D29V3, multiclass
                  clus
vv                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          31                526
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V4, continuous
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  31
  16Q GAIN WILD-TYPE   3 537
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   31
  16Q GAIN WILD-TYPE    3  537
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 0                  3
  YES               31                537
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  16Q GAIN MUTATED    2  1  0  1
  16Q GAIN WILD-TYPE 12 25  5  2
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                2                 12
  R1                1                 25
  R2                0                  5
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     0
  16Q GAIN WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q GAIN MUTATED                           2
  16Q GAIN WILD-TYPE                        30
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           0    25
  16Q GAIN WILD-TYPE                                         1   450
D29V7, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    0                 18
  BLACK OR AFRICAN AMERICAN                                2                 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   25                450
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0  16
  16Q GAIN WILD-TYPE  10 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0   16
  16Q GAIN WILD-TYPE   10  309
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               16                309
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    16   4
  17P GAIN WILD-TYPE 250 286
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                20                536 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                286 
$`17P GAIN MUTATED`
TCGA-09-0369 TCGA-09-2051 TCGA-13-0800 TCGA-13-0897 TCGA-13-0920 TCGA-13-1412 
       35.57        63.09         8.12        57.47        13.81         5.33 
TCGA-13-2057 TCGA-13-2060 TCGA-20-1683 TCGA-23-1114 TCGA-24-1845 TCGA-29-1763 
       14.24         8.61        25.38        68.68         3.81        66.81 
TCGA-29-2429 TCGA-36-1569 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2552 
        4.90        29.10        27.85        24.23        24.69        11.47 
TCGA-61-1900 TCGA-61-1904 
        5.79         9.07 

$`17P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       63.98        65.46        49.28        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       76.57        71.47        82.39        56.55        41.59        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       38.37       119.08        29.10        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 
       45.37        29.16         9.47        57.76        17.98         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       38.43        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 
       55.36        30.51        17.98         5.85         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       97.55         6.18         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       71.11        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.47        18.51        33.24        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
        3.91        35.44        35.80        15.12        19.86         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       24.59        44.55        39.58         2.73        12.39        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       15.19        17.82        55.17         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.54        34.06        32.25        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       38.93        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
        7.79         8.28         8.19        43.86        35.28        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 
       70.39        61.84        67.99        69.01        43.36        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        7.36         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       54.64        87.06        61.71        29.42        98.04        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       49.25         4.24        54.31        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       32.84        16.57         4.21         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
        2.56         3.91         3.09        12.23        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        6.28        54.77         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       72.20        27.52        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        42.54        40.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       49.41         8.81        29.13        18.90         2.24        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       54.51         3.22        31.20         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
      129.96         4.27         6.38        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        0.53        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 
       49.84         2.76         4.70         4.50         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.86         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        4.83        17.39        28.37        19.17        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
        8.55        72.92        12.46        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        3.45         1.18        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       16.21        56.58        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       47.70        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 
       48.33        38.24         8.32         3.48         3.72         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
       11.28         5.79         5.52         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       16.44        11.05        81.11         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       58.16        34.82       109.71        14.43        53.95        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       28.18        64.01        44.52        57.07        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       67.36        36.23        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        32.02        51.06        37.02         1.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        36.95        33.96         2.99        12.00 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.96        18.58        18.02        15.81         0.36        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
        7.86         0.30        56.94        60.59        35.54        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       14.96        24.99        18.05        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
        1.02        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       42.02         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       44.71        47.18       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       31.20        68.32         0.53        16.90        18.67        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        29.23        34.62        17.00        85.68 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.12        31.23        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       17.33        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        7.23         5.36        34.62        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11        42.25        11.84        11.47         9.76        21.04 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       38.07        51.91        36.26         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       48.10        44.91        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       18.77        22.49         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       28.77        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       25.74        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 
       20.52        14.17         6.05        16.18         7.99        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74         9.44        42.02         7.46        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       24.03        11.38        21.14         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       25.08        25.02       180.20        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
        9.40        34.39         2.14         5.42        44.81        20.52 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       11.11         8.09        20.94        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
        4.34        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 
        2.43        33.67        43.69         1.45         8.42        11.41 
TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       13.02        34.13        31.30        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       56.61        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        5.52        14.50        17.98         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       51.72        71.74        61.64        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              3.81               0.26 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             68.68             180.20 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            19.235             28.670 
[1] "3.8 - 68.7 (19.2)"  "0.3 - 180.2 (28.7)"
[1] "hr=" "2"  
D30V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  17P GAIN MUTATED         0    21                0
  17P GAIN WILD-TYPE       2   536                2
D30V3, multiclass
                  clus
vv                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          21                536
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V4, continuous
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  22
  17P GAIN WILD-TYPE   3 546
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   22
  17P GAIN WILD-TYPE    3  546
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                  3
  YES               22                546
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  17P GAIN MUTATED    1  1  0  0
  17P GAIN WILD-TYPE 13 25  5  3
D30V6, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 46 
        TCGA-04-1516         TCGA-04-1644         TCGA-13-0807 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-13-0911         TCGA-13-A5FT         TCGA-13-A5FU 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-24-2033         TCGA-29-2414         TCGA-29-2425 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-29-2427         TCGA-29-2428         TCGA-29-2431 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-29-2432         TCGA-29-2434         TCGA-29-2436 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-36-2529         TCGA-36-2530         TCGA-36-2532 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-36-2534         TCGA-36-2537         TCGA-36-2538 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-36-2540         TCGA-36-2542         TCGA-36-2543 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-36-2544         TCGA-36-2545         TCGA-36-2547 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-36-2548         TCGA-36-2549         TCGA-36-2551 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-3P-A9WA         TCGA-42-2582         TCGA-42-2587 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-42-2588         TCGA-42-2589         TCGA-42-2590 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-42-2593         TCGA-57-1993         TCGA-59-2363 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-59-2372         TCGA-61-2612         TCGA-61-2613 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-61-2614         TCGA-OY-A56P         TCGA-OY-A56Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-VG-A8LO 
"17P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     1
  17P GAIN WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P GAIN MUTATED                           2
  17P GAIN WILD-TYPE                        30
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0    15
  17P GAIN WILD-TYPE                                         1   460
D30V7, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    1                 17
  BLACK OR AFRICAN AMERICAN                                2                 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   15                460
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  11
  17P GAIN WILD-TYPE  10 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   11
  17P GAIN WILD-TYPE   10  314
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               11                314
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    24  22
  17Q GAIN WILD-TYPE 242 268
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                46                510 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                22                268 
$`17Q GAIN MUTATED`
TCGA-04-1337 TCGA-04-1362 TCGA-04-1530 TCGA-09-0369 TCGA-09-2051 TCGA-10-0936 
        2.01        44.32       119.08        35.57        63.09        35.80 
TCGA-13-0730 TCGA-13-0760 TCGA-13-0768 TCGA-13-0800 TCGA-13-0897 TCGA-13-0920 
       17.82        11.54         8.45         8.12        57.47        13.81 
TCGA-13-1408 TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1489 TCGA-13-2057 
        5.92         5.33        54.64        29.42        82.88        14.24 
TCGA-13-2060 TCGA-23-1109 TCGA-23-1114 TCGA-24-1464 TCGA-24-1844 TCGA-24-1845 
        8.61        51.35        68.68        12.46         3.72         3.81 
TCGA-24-1850 TCGA-24-2020 TCGA-24-2298 TCGA-25-1319 TCGA-25-2392 TCGA-29-1699 
        5.52       152.02        53.26        65.00         1.02         0.53 
TCGA-30-1862 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 TCGA-36-1580 
        6.12        29.10        21.53        22.55        27.85        24.23 
TCGA-36-1581 TCGA-36-2552 TCGA-42-2588 TCGA-42-2593 TCGA-61-1737 TCGA-61-1900 
       24.69        11.47         9.44         1.48        44.84         5.79 
TCGA-61-1913 TCGA-61-1914 TCGA-61-2098 TCGA-61-2612 
       48.92        56.61        65.52         6.35 

$`17Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00         1.81        49.15        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       65.46        49.28        32.52        33.67        76.57        71.47 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 
       82.39        56.55        41.59        19.99        38.37        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       84.20        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 
       36.23        31.86        47.70        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       57.76        17.98         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       41.62        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 
       35.15         4.54       112.41        71.11        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       33.24        32.28        11.70         3.91        35.44        15.12 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       19.86         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       12.39        31.10        15.19        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 
       11.38        34.06        32.25        31.04        21.40        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       36.72        28.70        30.35        19.59         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        43.86        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       68.94       107.18        91.40        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 
       61.84        67.99        69.01        43.36        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36        47.38        48.33        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       37.08        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 
        6.05         6.84         4.70         4.21        87.06        61.71 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       98.04        20.68        22.39        70.82        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       38.20        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       13.97        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 
        4.18         2.56         3.91         3.09        12.23        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.75         6.28        54.77         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       26.20        72.20        27.52        25.38        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
        2.93         2.66        47.54        42.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        31.76        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 
        2.24        54.51         3.22        31.20         4.57        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       86.01       129.96         4.27         6.38        39.09        33.47 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       58.13         0.53        24.95       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        5.36         4.83        17.39        28.37        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
       43.53         8.55        72.92        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        3.45         1.18        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       16.21        56.58        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       47.70        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 
       48.33        38.24         8.32         3.48         4.37        11.28 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.79         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
       81.11         4.87        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       14.43        53.95        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86         1.02        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       37.02         1.02        34.98        36.95        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       12.00         2.96        18.58        18.02        15.81         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       51.22        14.96        24.99        18.05        85.05        13.02 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       49.05        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       42.02         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       44.71        47.18       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32        16.90        18.67        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        29.23        34.62        17.00        85.68        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.12        31.23        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       17.33        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        7.23         5.36        34.62        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       45.11         4.90        42.25        11.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       21.04        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 
        0.26        48.10        44.91        34.78        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       18.77        22.49         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-2529 
       28.77        22.85         8.55        30.08        25.74        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       21.60         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 
        6.05        16.18         7.99        26.04        23.74        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
        7.46        40.77        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       44.81        20.52        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       35.80         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       42.51        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        5.52        14.50        17.98         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 
       51.72        71.74        61.64        58.39        60.62        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        6.48        76.87        20.68        44.52       125.75        22.22 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61        39.68        18.94         0.79         8.05 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.53               0.26 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            152.02             180.20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             22.04              28.67 
[1] "0.5 - 152.0 (22.0)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  17Q GAIN MUTATED         0    47                0
  17Q GAIN WILD-TYPE       2   510                2
D31V3, multiclass
                  clus
vv                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          47                510
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, continuous
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  47
  17Q GAIN WILD-TYPE   3 521
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   47
  17Q GAIN WILD-TYPE    3  521
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                  3
  YES               47                521
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN MUTATED    1  1  2  0
  17Q GAIN WILD-TYPE 13 25  3  3
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0                1                 13
  R1                1                 25
  R2                2                  3
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  1     2
  17Q GAIN WILD-TYPE                                2    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q GAIN MUTATED                           2
  17Q GAIN WILD-TYPE                        30
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    38
  17Q GAIN WILD-TYPE                                         1   437
D31V7, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                2                 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   38                437
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  27
  17Q GAIN WILD-TYPE  10 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   27
  17Q GAIN WILD-TYPE   10  298
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               27                298
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    65  51
  18P GAIN WILD-TYPE 201 239
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               116                440 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                51                239 
$`18P GAIN MUTATED`
TCGA-04-1332 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1361 TCGA-04-1371 
       41.00        65.52        63.09        21.57        32.52        82.39 
TCGA-04-1516 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 
       41.59        38.37        29.10        84.20        48.89        27.88 
TCGA-04-1652 TCGA-09-0369 TCGA-09-1665 TCGA-09-1668 TCGA-09-2055 TCGA-10-0930 
       31.86        35.57        41.62        55.36        26.93        33.24 
TCGA-10-0937 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 TCGA-13-0802 TCGA-13-0885 
       15.12        32.25         8.45        19.59         8.19        91.40 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0919 
       70.39        67.99        56.15        19.36        48.33        14.89 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1481 TCGA-13-1489 TCGA-13-1497 
        6.05         5.92         4.70        87.06        82.88        54.31 
TCGA-13-1499 TCGA-13-1504 TCGA-13-1507 TCGA-13-1510 TCGA-13-2057 TCGA-13-2059 
       38.40        16.57         4.77         2.56        14.24        12.23 
TCGA-13-2060 TCGA-20-0987 TCGA-20-1686 TCGA-23-1022 TCGA-23-1024 TCGA-23-1032 
        8.61        23.05         2.93        42.54        15.39         2.24 
TCGA-23-1110 TCGA-23-1114 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
       54.51        68.68         6.38        33.47        58.13         0.53 
TCGA-23-2077 TCGA-24-0968 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1466 
      115.89        19.66        17.39        28.37        18.67        45.14 
TCGA-24-1558 TCGA-24-1567 TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1850 
       19.53        17.23        38.24         3.72         3.81         5.52 
TCGA-24-1924 TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2261 
       30.21         4.87       152.02        34.82        53.95         0.79 
TCGA-24-2289 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1623 
       67.36        32.02        34.98        65.00        33.96        18.58 
TCGA-25-1628 TCGA-25-1635 TCGA-25-2400 TCGA-29-1695 TCGA-29-1698 TCGA-29-1711 
       20.61        51.22        42.02         0.79        68.32        34.62 
TCGA-29-1778 TCGA-29-1784 TCGA-29-2425 TCGA-29-2432 TCGA-29-2434 TCGA-30-1853 
       14.93         5.36        65.00        11.84        11.47        36.26 
TCGA-30-1866 TCGA-31-1959 TCGA-36-1581 TCGA-36-2537 TCGA-36-2547 TCGA-42-2589 
       36.62         2.20        24.69        25.91        20.52        42.02 
TCGA-57-1583 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2352 TCGA-59-2355 
       11.38        22.32        29.00        25.02         9.40         2.14 
TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1740 TCGA-61-1899 
        8.09        27.88         4.34        31.79         2.43         8.42 
TCGA-61-1907 TCGA-61-1917 TCGA-61-2008 TCGA-61-2018 TCGA-61-2096 TCGA-61-2111 
       31.30        43.43        30.64        45.40        58.39       125.75 
TCGA-61-2614 TCGA-WR-A838 
        8.61         8.05 

$`18P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24         1.81        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 
       11.87        48.76        63.98        65.46        49.28        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 TCGA-04-1530 
       33.67        76.57        71.47        56.55        19.99       119.08 
TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 
       55.43        28.64        64.64        36.23        47.70        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 
       29.16         9.47        57.76        17.98         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        57.60        61.87        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       35.15         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       20.94        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 
       32.28        11.70         3.91        35.44        35.80        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
        6.21        24.59        44.55        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.10        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 
       11.38        11.54        34.06        31.04        21.40        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       36.72        28.70        30.35         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.28        43.86        35.28        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 
      107.18        74.27        66.67        61.84        69.01        43.36 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       57.47        57.07        47.38        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       37.08        27.72        34.06        29.98        21.17        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 
        6.84         4.21         5.33        54.64        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       98.04        20.68        22.39        70.82        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
       38.20        49.25         4.24        37.61        13.97        32.84 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2061 
        4.21         4.41         4.18         3.91         3.09        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
        8.75         6.28        54.77         8.42        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 
       72.20        27.52        25.38        19.10        16.70         2.66 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       47.54        40.54        26.83        31.76        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
       29.13        18.90        51.35         3.22        31.20         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-2072 
       33.30        86.01       129.96         4.27        39.09        24.95 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       87.48        91.66        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        11.64        21.80        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 
        5.95         5.36         4.83        19.17        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        12.46       105.99         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       39.88        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 
       90.15        88.37        48.33         8.32         3.48         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 
       11.28         5.79         9.80        22.68        16.44        11.05 
TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 
       81.11        44.84        58.16       109.71        14.43        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 
       28.18        64.01        44.52        57.07        36.16         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 
       47.54        31.63        70.45        44.61         0.82        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       16.64        33.11        55.86        53.26         1.02        26.96 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
       51.06        37.02         1.02        36.95         2.99        12.00 
TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 
        2.96        18.02        15.81         0.36         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       56.94        60.59        35.54        14.96        24.99        18.05 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       85.05        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       12.00        45.01        19.99         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       26.99        78.90        44.71        47.18       101.79        38.53 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.70        31.20         0.53        16.90        18.67        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       18.25        41.98        29.23        17.00        85.68        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.12        31.23        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 
       17.33        12.36        11.84        12.30         8.38         7.23 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       34.62        86.17        62.47        45.11         4.90        42.25 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
        9.76        21.04        38.07        51.91         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 
        0.26        48.10        44.91        34.78         6.12         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 
       18.77        22.49         6.71        42.51        44.12        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       25.74        27.85        24.23        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       29.82        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       18.31        14.17         6.05        16.18        11.47         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       26.04        23.74         9.44         7.46        40.77         1.48 
TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 
       24.03        21.14         1.74        25.08       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
       22.32       116.12        34.39         5.42        44.81        20.52 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 
       11.11        20.94        31.43        18.54        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 
       44.84        35.80        33.67        43.69         1.45         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 
       11.41        13.02         9.07        34.13        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       48.92        56.61        67.76        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 
        5.52        14.50        17.98         4.01        39.85        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
        1.18        45.96         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       61.64        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P 
       20.68        44.52        22.22         6.35        31.07        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO 
       18.94         0.79 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.53               0.26 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            152.02             180.20 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            28.685             27.785 
[1] "0.5 - 152.0 (28.7)" "0.3 - 180.2 (27.8)"
[1] "hr=" "1.3"
D32V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18P GAIN MUTATED         0   117                0
  18P GAIN WILD-TYPE       2   440                2
D32V3, multiclass
                  clus
vv                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                         117                440
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, continuous
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0 119
  18P GAIN WILD-TYPE   3 449
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0  119
  18P GAIN WILD-TYPE    3  449
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 0                  3
  YES              119                449
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  18P GAIN MUTATED    4  5  0  0
  18P GAIN WILD-TYPE 10 21  5  3
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                4                 10
  R1                5                 21
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     3
  18P GAIN WILD-TYPE                                3    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED                           6
  18P GAIN WILD-TYPE                        26
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           0   103
  18P GAIN WILD-TYPE                                         1   372
D32V7, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                6                 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  103                372
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  66
  18P GAIN WILD-TYPE   8 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   66
  18P GAIN WILD-TYPE    8  259
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               66                259
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    38  32
  18Q GAIN WILD-TYPE 228 258
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                70                486 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                32                258 
$`18Q GAIN MUTATED`
TCGA-04-1346 TCGA-04-1349 TCGA-04-1516 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 
       65.52        21.57        41.59        29.10        84.20        48.89 
TCGA-04-1646 TCGA-04-1652 TCGA-09-0369 TCGA-09-1661 TCGA-09-1665 TCGA-09-1668 
       27.88        31.86        35.57        38.43        41.62        55.36 
TCGA-09-2055 TCGA-13-0717 TCGA-13-0762 TCGA-13-0795 TCGA-13-0802 TCGA-13-0890 
       26.93        24.59        32.25        19.59         8.19        67.99 
TCGA-13-0901 TCGA-13-0904 TCGA-13-0919 TCGA-13-1410 TCGA-13-1489 TCGA-13-1497 
       19.36        48.33        14.89         4.70        82.88        54.31 
TCGA-13-1504 TCGA-13-1507 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-23-1024 
       16.57         4.77         2.56        14.24         8.61        15.39 
TCGA-23-1114 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-24-0968 TCGA-24-1430 
       68.68        33.47         0.53       115.89        19.66        28.37 
TCGA-24-1434 TCGA-24-1466 TCGA-24-1604 TCGA-24-1845 TCGA-24-1924 TCGA-24-2019 
       18.67        45.14        88.37         3.81        30.21         4.87 
TCGA-24-2026 TCGA-24-2030 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1635 
       34.82        53.95        32.02        34.98        65.00        51.22 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1705 TCGA-29-1778 TCGA-29-1784 TCGA-29-2432 
        0.79        68.32        18.25        14.93         5.36        11.84 
TCGA-30-1853 TCGA-36-1581 TCGA-36-2537 TCGA-61-1722 TCGA-61-1728 TCGA-61-1733 
       36.26        24.69        25.91         8.09        27.88        31.79 
TCGA-61-1740 TCGA-61-1899 TCGA-61-1907 TCGA-61-1917 TCGA-61-1998 TCGA-61-2008 
        2.43         8.42        31.30        43.43         5.52        30.64 
TCGA-61-2096 TCGA-61-2101 TCGA-61-2111 TCGA-61-2614 
       58.39        55.50       125.75         8.61 

$`18Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 
       18.51        11.87        63.09        48.76        63.98        65.46 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       49.28        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 
       82.39        56.55        19.99        38.37       119.08        55.43 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        47.70        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 
        9.47        57.76        17.98         9.99        89.33        74.93 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       57.60        61.87        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        8.55        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 
      112.41        71.11        63.09        39.75        20.94        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       54.31        25.91        81.47        18.51        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       11.70         3.91        35.44        35.80        15.12        19.86 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
        6.21        44.55        39.58         2.73        12.39        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       15.19        17.82        55.17         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.54        34.06        31.04        21.40         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       36.72        28.70        30.35         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.28        43.86        35.28        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
      107.18        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 
       69.01        43.36        57.47        56.15        57.07        47.38 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        13.81         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       10.88         6.61         7.36         6.05         5.92         6.84 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       98.04        20.68        22.39        70.82        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       38.20        49.25         4.24        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 
       32.84         4.21         4.41         4.18         3.91         3.09 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
       12.23        10.78         8.75         6.28        54.77         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       23.05        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       19.10        16.70         2.93         2.66        47.54        42.54 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       18.90         2.24        51.35        54.51         3.22        31.20 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
        4.57        33.30        86.01       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1124 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       39.09        58.13        24.95        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       49.84         2.76         4.70         4.50         7.63        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       47.41         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       17.39        19.17        43.53         8.55        72.92        12.46 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
      105.99         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       90.15        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       16.44        11.05        81.11       152.02        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
      109.71        14.43        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 
       33.11        55.86        53.26         1.02        26.96        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       37.02         1.02        36.95        33.96         2.99        12.00 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.96        18.58        18.02        15.81         0.36        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 
        7.86         0.30        56.94        60.59        35.54        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       24.99        18.05        85.05        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       38.04         3.02        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        44.71 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 
       47.18       101.79        38.53        33.70        31.20         0.53 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       16.90        18.67        59.67        41.98        29.23        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       17.00        85.68        66.81        62.93        39.12        31.23 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
       12.30         8.38         7.23        34.62        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 
       62.47        45.11         4.90        42.25        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       21.04        38.07        51.91         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       48.10        44.91        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       18.77        22.49         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       28.77        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 
       30.08        25.74        27.85        24.23        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.49        29.82        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       20.98        18.31        20.52        14.17         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       11.47         7.99        26.04        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
        7.46        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.74        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
        5.42        44.81        20.52        11.11        20.94        31.43 
TCGA-61-1727 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       18.54         4.34        28.47        48.79        44.84        35.80 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       33.67        43.69         1.45         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
        9.07        34.13        37.05        42.51        48.92        56.61 
TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 
       67.76        15.75        38.17         2.01        14.50        17.98 
TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        4.01        39.85        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
        4.80         4.77        51.72        71.74        61.64        60.62 
TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 
       65.52         6.48        76.87        20.68        44.52        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        6.35        31.07        39.68        18.94         0.79         8.05 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.53               0.26 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            125.75             180.20 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            29.655             27.620 
[1] "0.5 - 125.8 (29.7)" "0.3 - 180.2 (27.6)"
[1] "hr=" "1.2"
D33V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18Q GAIN MUTATED         0    71                0
  18Q GAIN WILD-TYPE       2   486                2
D33V3, multiclass
                  clus
vv                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          71                486
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, continuous
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  72
  18Q GAIN WILD-TYPE   3 496
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   72
  18Q GAIN WILD-TYPE    3  496
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 0                  3
  YES               72                496
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  18Q GAIN MUTATED    1  4  0  0
  18Q GAIN WILD-TYPE 13 22  5  3
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                1                 13
  R1                4                 22
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     3
  18Q GAIN WILD-TYPE                                3    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q GAIN MUTATED                           2
  18Q GAIN WILD-TYPE                        30
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           0    64
  18Q GAIN WILD-TYPE                                         1   411
D33V7, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                2                 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   64                411
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  40
  18Q GAIN WILD-TYPE  10 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   40
  18Q GAIN WILD-TYPE   10  285
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               40                285
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    85  78
  19P GAIN WILD-TYPE 181 212
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               163                393 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                78                212 
$`19P GAIN MUTATED`
TCGA-04-1335 TCGA-04-1338 TCGA-04-1346 TCGA-04-1514 TCGA-04-1525 TCGA-04-1542 
        1.81        46.62        65.52        56.55        38.37        84.20 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-09-0367 TCGA-09-0369 TCGA-09-1665 
       28.64        64.64        31.86        17.98        35.57        41.62 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       61.87        30.51        17.98         8.55        97.55         6.18 
TCGA-09-2054 TCGA-10-0926 TCGA-10-0933 TCGA-10-0938 TCGA-13-0727 TCGA-13-0751 
       20.94        25.91        11.70        19.86        15.19        55.17 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0791 TCGA-13-0802 
       11.38        11.54        34.06        31.04        38.93         8.19 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0905 
       13.61        68.94       107.18        66.67        70.39        47.84 
TCGA-13-0920 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1481 TCGA-13-1482 
       13.81         6.05         5.92         4.70        87.06        61.71 
TCGA-13-1484 TCGA-13-1491 TCGA-13-1495 TCGA-13-1501 TCGA-13-1506 TCGA-13-1510 
       98.04        52.44        49.25        32.84         4.41         2.56 
TCGA-13-2057 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1686 
       14.24        23.05        25.94        26.20        27.52         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1109 
        2.66        47.54        42.54        15.39        26.83        51.35 
TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 TCGA-23-1809 
        3.22         4.57        33.30        86.01         6.38         0.53 
TCGA-23-2645 TCGA-24-1105 TCGA-24-1417 TCGA-24-1426 TCGA-24-1428 TCGA-24-1436 
        4.50        47.41         7.82         5.36        17.39         8.55 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1545 TCGA-24-1548 TCGA-24-1551 TCGA-24-1557 
        9.11         1.18        57.40        16.21        51.91        39.88 
TCGA-24-1558 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       19.53        48.33        38.24         3.48         3.72         3.81 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1928 TCGA-24-2020 TCGA-24-2030 
        5.52         9.80        22.68        11.05       152.02        53.95 
TCGA-24-2033 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2295 
       18.48         0.79        47.54        70.45        44.61        33.11 
TCGA-25-1312 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
        1.02        32.02        34.98        65.00        36.95        33.96 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-2398 TCGA-29-1695 TCGA-29-1698 
       12.00         2.96        18.58        45.01         0.79        68.32 
TCGA-29-1702 TCGA-29-1711 TCGA-29-1770 TCGA-29-1775 TCGA-29-1783 TCGA-29-1785 
       18.67        34.62        24.36        12.36         7.23        34.62 
TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1855 TCGA-30-1857 
       11.84        11.47        21.04        38.07         2.47         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1892 TCGA-31-1944 
       48.10        44.91         6.12         1.22        48.79        45.57 
TCGA-31-1950 TCGA-36-1578 TCGA-36-2529 TCGA-36-2534 TCGA-36-2543 TCGA-36-2544 
       18.77        27.85        35.05        29.82         2.24        20.98 
TCGA-36-2547 TCGA-36-2552 TCGA-42-2582 TCGA-42-2589 TCGA-57-1582 TCGA-57-1583 
       20.52        11.47        26.04        42.02        24.03        11.38 
TCGA-57-1586 TCGA-59-2348 TCGA-59-2351 TCGA-59-2355 TCGA-61-1725 TCGA-61-1728 
       22.32       180.20       116.12         2.14        31.43        27.88 
TCGA-61-1730 TCGA-61-1741 TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 
        4.34        33.67         8.42         9.07        34.13        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-2000 TCGA-61-2009 TCGA-61-2012 
       48.92        56.61        15.75        14.50        39.85        30.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 
       58.39        60.62        65.52        76.87       125.75        22.22 
TCGA-WR-A838 
        8.05 

$`19P GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       40.24        41.00        49.15         2.01        18.51        11.87 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       63.09        48.76        21.57        63.98        65.46        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       32.52        44.32        33.67        76.57        71.47        82.39 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 
       41.59        19.99       119.08        29.10        55.43        48.89 
TCGA-04-1646 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 
       27.88        36.23        47.70        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       57.76         9.99        38.43        89.33        74.93        57.60 
TCGA-09-1668 TCGA-09-1672 TCGA-09-1673 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
       55.36         5.85         3.02         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 
      112.41        71.11        63.09        39.75        26.93        12.46 
TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 
       54.31        81.47        18.51        33.24        32.28         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        35.80        15.12         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 
       39.58         2.73        12.39        31.10        17.82         2.50 
TCGA-13-0757 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 
       11.18        32.25        21.40         8.45        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       30.35        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0885 TCGA-13-0886 TCGA-13-0889 
       43.86        35.28        35.28        91.40        74.27        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       67.99        69.01        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36        47.38        48.33        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       27.72        34.06        29.98        21.17        14.89         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 
        6.41         6.08        10.88         6.61         7.36         6.84 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 
        4.21         5.33        54.64        29.42        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 
       70.82        82.88        73.55        38.20         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 
       37.61        38.40        13.97        16.57         4.21         4.77 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
        4.18         3.91         3.09        12.23         8.61        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0996 TCGA-20-1683 
        8.75         6.28        54.77         8.42        72.20        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       19.10        16.70        40.54        31.76        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
       29.13        18.90         2.24        54.51        31.20        68.68 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
      129.96         4.27        39.09        33.47        58.13        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.70         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 
        7.66        22.32        54.12        63.55         6.31         6.38 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 
        4.83        28.37        19.17        18.67        43.53        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 
       12.46        45.14       105.99         3.45        22.22        26.96 
TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       64.27        56.58        41.06        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       70.62        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1842 TCGA-24-1846 TCGA-24-1847 
       17.23        90.15        88.37         8.32         4.37        11.28 
TCGA-24-1849 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 
        5.79        30.21        16.44        81.11         4.87        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 
       58.16        34.82       109.71        14.43        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 TCGA-24-2288 
       44.52        57.07        36.16         0.36        31.63         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 
       67.36        36.23        16.64        55.86        53.26        26.96 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1322 TCGA-25-1625 TCGA-25-1626 
       51.06        37.02         1.02         2.99        18.02        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
        0.36        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       35.54        51.22        14.96        24.99        18.05        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       78.90        44.71        47.18       101.79        38.53        33.70 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       31.20         0.53        16.90        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       29.23        17.00        85.68        66.81        62.93        39.12 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 
       31.23        22.98        22.55        17.33        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
       14.93         8.38         5.36        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-30-1718 TCGA-30-1853 
       45.11         4.90        42.25         9.76        51.91        36.26 
TCGA-30-1856 TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
       15.68        34.78        36.62        57.57        24.26        30.05 
TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       30.18        22.49         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       28.77        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 
       30.08        25.74        24.23        24.69        33.01        29.49 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2545 TCGA-36-2548 
       25.91        25.08        23.80        21.60        18.31        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
        6.05        16.18         7.99        23.74         9.44         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 
       40.77         1.48        21.14         1.74        29.00        25.08 
TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 
       25.02        80.12        22.32         9.40        34.39         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 
       44.81        20.52        11.11         8.09        20.94        18.54 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       31.79        28.47        48.79        44.84        35.80         2.43 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 
       43.69         1.45         5.79        11.41        13.02        31.30 
TCGA-61-1910 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       37.05        67.76        43.43        38.17         2.01         5.52 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       17.98         4.01        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2101 
        4.80         4.77        51.72        71.74        61.64        55.50 
TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
        6.48        20.68        44.52         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       39.68        18.94         0.79 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.26               0.30 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            180.20             129.96 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             26.20              28.77 
[1] "0.3 - 180.2 (26.2)" "0.3 - 130.0 (28.8)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  19P GAIN MUTATED         0   164                1
  19P GAIN WILD-TYPE       2   393                1
D34V3, multiclass
                  clus
vv                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                         164                393
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, continuous
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     2 166
  19P GAIN WILD-TYPE   1 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2  166
  19P GAIN WILD-TYPE    1  402
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 2                  1
  YES              166                402
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED    5  7  0  0
  19P GAIN WILD-TYPE  9 19  5  3
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                5                  9
  R1                7                 19
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     4
  19P GAIN WILD-TYPE                                3    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED                           6
  19P GAIN WILD-TYPE                        26
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           1   142
  19P GAIN WILD-TYPE                                         0   333
D34V7, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                6                 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  142                333
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     2  96
  19P GAIN WILD-TYPE   8 229
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   96
  19P GAIN WILD-TYPE    8  229
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               96                229
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    76  79
  19Q GAIN WILD-TYPE 190 211
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               155                401 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                79                211 
$`19Q GAIN MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1516 TCGA-04-1517 
       41.00        46.62        11.87        65.52        41.59        19.99 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1648 TCGA-04-1652 TCGA-09-0364 
       38.37        29.10        84.20        28.64        31.86        29.16 
TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 
        9.47        17.98        35.57        30.51        17.98         8.55 
TCGA-09-2043 TCGA-10-0926 TCGA-10-0933 TCGA-13-0717 TCGA-13-0727 TCGA-13-0751 
        6.18        25.91        11.70        24.59        15.19        55.17 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0791 TCGA-13-0794 TCGA-13-0802 
       11.38        11.54        34.06        38.93        30.35         8.19 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0888 TCGA-13-0905 TCGA-13-0920 TCGA-13-1408 
       68.94        91.40        70.39        47.84        13.81         5.92 
TCGA-13-1410 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1491 TCGA-13-1492 
        4.70        87.06        61.71        98.04        52.44        73.55 
TCGA-13-1495 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-20-0987 
       49.25        32.84        16.57         4.41         4.77        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1687 TCGA-23-1022 TCGA-23-1026 
       25.94        26.20        27.52         2.66        42.54        26.83 
TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 TCGA-23-1809 
        3.22         4.57        33.30        86.01         6.38         0.53 
TCGA-23-2645 TCGA-24-1105 TCGA-24-1417 TCGA-24-1426 TCGA-24-1428 TCGA-24-1436 
        4.50        47.41         7.82         5.36        17.39         8.55 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 
        9.11         1.18        57.40        16.21        41.06        51.91 
TCGA-24-1552 TCGA-24-1557 TCGA-24-1558 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 
       41.39        39.88        19.53        48.33        38.24         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-2020 
        3.72         3.81        11.28         5.52        22.68       152.02 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 
       53.95        18.48         0.79        47.54        70.45        44.61 
TCGA-24-2288 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 
        0.82        33.11         1.02        32.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       65.00        36.95        33.96        12.00         2.96        18.58 
TCGA-25-2398 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1766 
       45.01        47.18         0.79        68.32        16.90        39.12 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1785 TCGA-29-2432 TCGA-29-2434 
       24.36        17.33        12.36        34.62        11.84        11.47 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 
       21.04        38.07        51.91         2.47         0.26        48.10 
TCGA-30-1860 TCGA-30-1867 TCGA-30-1892 TCGA-31-1944 TCGA-31-1959 TCGA-36-1578 
       44.91         1.22        48.79        45.57         2.20        27.85 
TCGA-36-2529 TCGA-36-2534 TCGA-36-2543 TCGA-36-2544 TCGA-36-2552 TCGA-42-2582 
       35.05        29.82         2.24        20.98        11.47        26.04 
TCGA-42-2589 TCGA-57-1582 TCGA-57-1586 TCGA-59-2348 TCGA-59-2351 TCGA-59-2355 
       42.02        24.03        22.32       180.20       116.12         2.14 
TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1741 TCGA-61-1904 TCGA-61-1906 
        8.09        27.88         4.34        33.67         9.07        34.13 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-2009 TCGA-61-2012 
       42.51        48.92        56.61        15.75        39.85        30.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2113 TCGA-WR-A838 
       58.39        60.62        65.52        22.22         8.05 

$`19Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1347 
       40.24         1.81        49.15         2.01        18.51        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       48.76        21.57        63.98        65.46        49.28        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       44.32        33.67        76.57        71.47        82.39        56.55 
TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 TCGA-04-1651 
      119.08        55.43        48.89        27.88        64.64        36.23 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       47.70        45.37        57.76         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1672 
       74.93        41.62        57.60        61.87        55.36         5.85 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
        3.02        97.55         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 
       54.31        81.47        18.51        33.24        32.28         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 
       35.44        35.80        15.12        19.86         6.21        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 
       39.58         2.73        12.39        31.10        17.82         2.50 
TCGA-13-0757 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 
       11.18        32.25        31.04        21.40         8.45        36.72 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       28.70        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0886 
       43.86        35.28        35.28        13.61       107.18        74.27 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       66.67        61.84        67.99        69.01        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 
       56.15        57.07        19.36        47.38        48.33        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        7.36         6.05         6.84         4.21         5.33        54.64 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1494 
       29.42        20.68        22.39        70.82        82.88        38.20 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1505 
        4.24        54.31        37.61        38.40        13.97         4.21 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.18         2.56         3.91         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        8.61        10.78         8.75         6.28        54.77         8.42 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
       72.20        25.38        19.10        16.70         2.93        47.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        15.39        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
       18.90         2.24        51.35        54.51        31.20        68.68 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
      129.96         4.27        39.09        33.47        58.13        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.70         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 
        7.66        22.32        54.12        63.55         6.31         6.38 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 
        4.83        28.37        19.17        18.67        43.53        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 
       12.46        45.14       105.99         3.45        22.22        26.96 
TCGA-24-1546 TCGA-24-1549 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 
       64.27        56.58        58.09        88.50        70.62        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1842 TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 TCGA-24-1924 
       88.37         8.32         4.37         5.79         9.80        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 
       16.44        11.05        81.11         4.87        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       34.82       109.71        14.43        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 TCGA-24-2289 TCGA-24-2290 
       57.07        36.16         0.36        31.63        67.36        36.23 
TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       16.64        55.86        53.26        26.96        51.06        37.02 
TCGA-25-1322 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
        2.99        18.02        15.81         0.36        20.61         7.86 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        56.94        60.59        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       24.99        18.05        85.05        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
       38.04         3.02        12.00        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
       29.03        31.00        26.99        78.90        44.71       101.79 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 
       38.53        33.70        31.20         0.53        18.67        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        29.23        34.62        17.00        85.68 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 
       66.81        62.93        31.23        22.98        22.55        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 
       12.30        14.93         8.38         7.23         5.36        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 
       65.00        62.47        45.11         4.90        42.25         9.76 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1880 
       36.26        15.68        34.78         6.12        36.62        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       24.26        30.05        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       42.51        44.12        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 
       22.55         8.55        30.08        25.74        24.23        24.69 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       33.01        29.49        25.91        25.08        23.80        21.60 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA 
       18.31        20.52        14.17         6.05        16.18         7.99 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 
       23.74         9.44         7.46        40.77         1.48        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 
       21.14         1.74        29.00        25.08        25.02        80.12 
TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
       22.32         9.40        34.39         5.42        44.81        20.52 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1733 TCGA-61-1734 
       11.11        20.94        31.43        18.54        31.79        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 
       48.79        44.84        35.80         2.43        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 
        8.42         5.79        11.41        13.02        31.30        37.05 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       67.76        43.43        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       17.98         4.01        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2101 
        4.80         4.77        51.72        71.74        61.64        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2612 
        6.48        76.87        20.68        44.52       125.75         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       31.07         8.61        39.68        18.94         0.79 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.26               0.30 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            180.20             129.96 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             27.52              28.47 
[1] "0.3 - 180.2 (27.5)" "0.3 - 130.0 (28.5)"
[1] "hr=" "1"  
D35V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  19Q GAIN MUTATED         0   156                2
  19Q GAIN WILD-TYPE       2   401                0
D35V3, multiclass
                  clus
vv                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                         156                401
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, continuous
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2 158
  19Q GAIN WILD-TYPE   1 410
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2  158
  19Q GAIN WILD-TYPE    1  410
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 2                  1
  YES              158                410
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED    5  6  0  0
  19Q GAIN WILD-TYPE  9 20  5  3
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                5                  9
  R1                6                 20
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     4
  19Q GAIN WILD-TYPE                                3    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q GAIN MUTATED                           3
  19Q GAIN WILD-TYPE                        29
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           1   139
  19Q GAIN WILD-TYPE                                         0   336
D35V7, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                3                 29
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  139                336
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2  89
  19Q GAIN WILD-TYPE   8 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   89
  19Q GAIN WILD-TYPE    8  236
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               89                236
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   117 162
  20P GAIN WILD-TYPE 149 128
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               279                277 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               162                128 
$`20P GAIN MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       40.24        41.00         2.01        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1364 
       63.09        21.57        63.98        65.46        49.28        33.67 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1655 
       56.55        19.99        84.20        27.88        64.64        45.37 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 
       57.76        17.98        35.57         9.99        38.43        41.62 
TCGA-09-1668 TCGA-09-1670 TCGA-09-1674 TCGA-09-2043 TCGA-09-2051 TCGA-09-2053 
       55.36        17.98         8.55         6.18        63.09        39.75 
TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 
       11.70        35.44        35.80        19.86        24.59        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 
        2.73        12.39        15.19        55.17        11.18        11.38 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0794 TCGA-13-0800 
       11.54        32.25        31.04        21.40        30.35         8.12 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
        8.19        43.86       107.18        91.40        66.67        70.39 
TCGA-13-0890 TCGA-13-0899 TCGA-13-0904 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 
       67.99        56.15        48.33        29.98        14.89        13.81 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1481 
        6.41         6.08         6.05         5.92         6.84        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1492 
       61.71        98.04        20.68        22.39        70.82        73.55 
TCGA-13-1497 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       54.31        38.40        16.57         4.21         4.41         4.77 
TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
       14.24        10.78         8.75         8.42        25.94        26.20 
TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1024 TCGA-23-1031 TCGA-23-1032 
       16.70         2.93        47.54        15.39        18.90         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1121 TCGA-23-1122 
       51.35        54.51         3.22        68.68         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2084 TCGA-23-2643 
       33.47        58.13         0.53       115.89        49.84         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 
        4.50         7.63        21.80        22.32        47.41         6.31 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 
        0.76         6.25         6.02         4.83        28.37        19.17 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 
       18.67         8.55        12.46        45.14         9.11        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1553 TCGA-24-1556 
       26.96        57.40        64.27        16.21        58.09        70.62 
TCGA-24-1557 TCGA-24-1564 TCGA-24-1604 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       39.88        25.87        88.37         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-1928 TCGA-24-1930 
        3.81        11.28         5.52        22.68        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 
        4.87       152.02        34.82       109.71        53.95        18.48 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       36.16         0.79        47.54        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 
       67.36        36.23        16.64        33.11         1.02        26.96 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 
        2.99        12.00         2.96        18.58        15.81         0.36 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       20.61         0.30        56.94        60.59        35.54        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 
       14.96        24.99        18.05        85.05        38.04         3.02 
TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1691 
       45.01        42.02        29.03        31.00        78.90        47.18 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 
        0.79        31.20        68.32         0.53        16.90        59.67 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       41.98        29.23        17.00        66.81        62.93        39.12 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 
       22.98        24.36        12.36        14.93         7.23         5.36 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-A5NZ 
       86.17        65.00        45.11         4.90        42.25        21.04 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
       38.07        51.91        36.26         2.47        15.68        48.10 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1892 TCGA-31-1950 
       34.78         6.12        36.62         1.22        48.79        18.77 
TCGA-31-1951 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 
       22.49        42.51         2.20        28.77        29.10        22.85 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-2534 TCGA-36-2547 TCGA-36-2548 
        8.55        30.08        24.23        29.82        20.52        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 
       16.18        11.47        23.74         7.46         1.48        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 
        1.74        22.32       116.12         9.40         2.14         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 
       44.81        20.52         8.09        18.54         4.34        31.79 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
       43.69         8.42         5.79        13.02         9.07        34.13 
TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       42.51        56.61        67.76        43.43        15.75        38.17 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2097 TCGA-61-2098 
        4.01        30.64        39.85        30.64        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 
       55.50         6.48        76.87        22.22         6.35         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       39.68        18.94         0.79 

$`20P GAIN WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1348 TCGA-04-1361 TCGA-04-1362 
        1.81        49.15        46.62        48.76        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 
       76.57        71.47        82.39        41.59        38.37       119.08 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 
       29.10        55.43        48.89        28.64        36.23        31.86 
TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       47.70        29.16         9.47        89.33        74.93        57.60 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 
       61.87        30.51         5.85         3.02        97.55         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 
       35.15         4.54       112.41        71.11        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        54.31        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0726 
       32.28         3.91        15.12         6.21        44.55        31.10 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0761 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       17.82         2.50        34.06         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0804 
       28.70        19.59         8.71         7.79         8.28        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 TCGA-13-0891 
       35.28        13.61        68.94        74.27        61.84        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 
       43.36        57.47        57.07        19.36        47.38        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 
       44.94        44.84        37.08        27.72        34.06        21.17 
TCGA-13-0921 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1410 TCGA-13-1411 
        4.64        10.88         6.61         7.36         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 
        5.33        54.64        29.42        82.88        52.44        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1509 
       49.25         4.24        37.61        13.97        32.84         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2071 
        2.56         3.91         3.09        12.23         8.61         6.28 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
       54.77        23.05        72.20        27.52        25.38        19.10 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
        2.66        42.54        40.54        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
        8.81        29.13        31.20         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
      129.96         4.27        24.95        87.48        91.66        77.00 
TCGA-23-2641 TCGA-24-0968 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
        2.76        19.66        11.64        41.56         7.66        54.12 
TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1425 
       63.55         6.38         7.82         7.99         7.86         5.95 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 
        5.36        17.39        43.53        72.92       105.99         3.45 
TCGA-24-1471 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 
        1.18        56.58        41.06        51.91        41.39        88.50 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 
       19.53        44.09        45.50        47.70        10.26        17.23 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 
       90.15        48.33        38.24         4.37         5.79         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2035 
       30.21        16.44        44.84        58.16        14.43        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2297 
       64.01        44.52        57.07         0.36        31.63        55.86 
TCGA-24-2298 TCGA-25-1314 TCGA-25-1315 TCGA-25-1625 TCGA-25-1630 TCGA-25-2042 
       53.26        32.02        51.06        18.02         7.86        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 
       49.05         1.02        12.00        19.99         2.96        26.99 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1702 TCGA-29-1705 
       44.71       101.79        38.53        33.70        18.67        18.25 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 
       34.62        85.68        31.23        22.55        17.33        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 TCGA-29-2432 TCGA-29-2434 
       12.30         8.38        34.62        62.47        11.84        11.47 
TCGA-29-2436 TCGA-30-1857 TCGA-30-1860 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
        9.76         0.26        44.91        57.57        24.26        30.05 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1953 TCGA-31-1956 TCGA-36-1570 TCGA-36-1574 
       45.57        30.18         6.71        44.12        21.53        22.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       25.74        27.85        24.69        35.05        33.01        29.49 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       25.91        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 
       18.31         6.05         7.99        26.04         9.44        42.02 
TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       40.77        24.03        21.14        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-61-1721 TCGA-61-1724 
      180.20        80.12        22.32        34.39        11.11        20.94 
TCGA-61-1725 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       31.43        27.88        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1901 TCGA-61-1907 TCGA-61-1910 
        2.43        33.67         1.45        11.41        31.30        37.05 
TCGA-61-1913 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2016 
       48.92         2.01         5.52        14.50        17.98         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 
       61.64        58.39        20.68        44.52       125.75        31.07 
TCGA-WR-A838 
        8.05 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.30               0.26 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            152.02             180.20 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             24.36              29.42 
[1] "0.3 - 152.0 (24.4)" "0.3 - 180.2 (29.4)"
[1] "hr=" "1.4"
D36V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20P GAIN MUTATED         2   279                1
  20P GAIN WILD-TYPE       0   278                1
D36V3, multiclass
                  clus
vv                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  OMENTUM                         2                  0
  OVARY                         279                278
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, continuous
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2 284
  20P GAIN WILD-TYPE   1 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  284
  20P GAIN WILD-TYPE    1  284
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 2                  1
  YES              284                284
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED    5 12  4  1
  20P GAIN WILD-TYPE  9 14  1  2
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0                5                  9
  R1               12                 14
  R2                4                  1
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  2     5
  20P GAIN WILD-TYPE                                1    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P GAIN MUTATED                          17
  20P GAIN WILD-TYPE                        15
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           1   242
  20P GAIN WILD-TYPE                                         0   233
D36V7, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  1
  ASIAN                                                    5                 13
  BLACK OR AFRICAN AMERICAN                               17                 15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  242                233
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     4 158
  20P GAIN WILD-TYPE   6 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4  158
  20P GAIN WILD-TYPE    6  167
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              158                167
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   143 173
  20Q GAIN WILD-TYPE 123 117
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               316                240 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               173                117 
$`20Q GAIN MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       40.24        41.00         2.01        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1364 
       63.09        21.57        63.98        65.46        49.28        33.67 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1542 TCGA-04-1646 
       82.39        56.55        19.99        38.37        84.20        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 
       28.64        64.64        31.86        45.37        29.16        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 TCGA-09-1668 
       17.98        35.57         9.99        38.43        41.62        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-2051 TCGA-09-2053 TCGA-10-0933 
       30.51        17.98         8.55        63.09        39.75        11.70 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 
       35.44        35.80        19.86        24.59        39.58         2.73 
TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 
       12.39        15.19        17.82        55.17        11.18        11.38 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0766 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 
       11.54        32.25        21.40        30.35        19.59         8.12 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
        8.19        43.86       107.18        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 TCGA-13-0905 
       70.39        67.99        43.36        56.15        19.36        47.84 
TCGA-13-0906 TCGA-13-0911 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 
       44.94        27.72        29.98        14.89        13.81         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.08        10.88         6.05         5.92         6.84         4.70 
TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
        5.33        87.06        61.71        98.04        20.68        22.39 
TCGA-13-1492 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       73.55        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU 
        4.77        14.24         8.61        10.78         8.75         8.42 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
       25.94        26.20        27.52        16.70         2.93        47.54 
TCGA-23-1022 TCGA-23-1024 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       42.54        15.39        18.90         2.24        51.35        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1121 TCGA-23-1122 
        3.22        68.68         4.57        33.30         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 
       33.47        58.13         0.53       115.89        91.66        49.84 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0975 TCGA-24-0982 
        4.70         4.50         7.63        19.66        21.80        22.32 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 
       54.12        47.41         6.31         7.82         7.99         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1431 TCGA-24-1434 
        6.25         6.02         5.36         4.83        19.17        18.67 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 
        8.55        12.46        45.14         9.11        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 
       57.40        64.27        16.21        58.09        70.62        39.88 
TCGA-24-1558 TCGA-24-1604 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       19.53        88.37         8.32         3.48         3.72         3.81 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
       11.28         5.79         5.52         9.80        22.68        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2027 
       11.05        81.11         4.87       152.02        34.82       109.71 
TCGA-24-2033 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 
       18.48        36.16         0.79        47.54        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 
        0.82        67.36        36.23        16.64        33.11         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       26.96        32.02        37.02         1.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       36.95        33.96         2.99        12.00         2.96        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       15.81         0.36        20.61         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       35.54        51.22        14.96        24.99        18.05        85.05 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 
       38.04         3.02        45.01        42.02        29.03        31.00 
TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       78.90        47.18       101.79        31.20        68.32         0.53 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 
       16.90        59.67        18.25        41.98        29.23        17.00 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 
       66.81        62.93        39.12        22.98        24.36        17.33 
TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 
       12.36        14.93         7.23         5.36        86.17        65.00 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       45.11         4.90        42.25         9.76        21.04        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1861 
       51.91        36.26         2.47        15.68        48.10        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
        6.12        36.62         1.22        24.26        48.79        45.57 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 TCGA-36-1571 
       18.77        22.49        42.51         2.20        29.10        22.85 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2534 TCGA-36-2547 
        8.55        30.08        24.23        24.69        29.82        20.52 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2591 
       14.17        16.18        11.47         7.99        23.74        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
        1.48        24.03        11.38         1.74        22.32        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 
       25.08        25.02       116.12         9.40         2.14        44.81 
TCGA-59-A5PD TCGA-61-1722 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       20.52         8.09        18.54        27.88         4.34        31.79 
TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 
       44.84        33.67        43.69         8.42         5.79        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
        9.07        34.13        42.51        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2097 
       15.75        38.17         4.01        39.85        30.64        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2113 TCGA-61-2612 
       65.52        55.50         6.48        76.87        22.22         6.35 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        8.61        39.68        18.94         0.79 

$`20Q GAIN WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1348 TCGA-04-1361 TCGA-04-1362 
        1.81        49.15        46.62        48.76        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1516 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 
       76.57        71.47        41.59       119.08        29.10        55.43 
TCGA-04-1644 TCGA-04-1651 TCGA-04-1654 TCGA-09-0365 TCGA-09-1662 TCGA-09-1664 
       48.89        36.23        47.70         9.47        89.33        74.93 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 
       57.60        61.87         5.85         3.02        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 
        6.12        35.15         4.54       112.41        71.11        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 
       33.24        32.28         3.91        15.12         6.21        44.55 
TCGA-13-0726 TCGA-13-0755 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 
       31.10         2.50        34.06        31.04         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0804 
       36.72        28.70         8.71         7.79         8.28        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0889 TCGA-13-0891 TCGA-13-0897 
       35.28        13.61        68.94        61.84        69.01        57.47 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 
       57.07        47.38        48.33        44.84        37.08        34.06 
TCGA-13-0916 TCGA-13-0921 TCGA-13-1404 TCGA-13-1405 TCGA-13-1411 TCGA-13-1477 
       21.17         4.64         6.61         7.36         4.21        54.64 
TCGA-13-1483 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 
       29.42        70.82        82.88        52.44        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1509 TCGA-13-1510 
        4.24        54.31        37.61        13.97         4.18         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 
        3.91         3.09        12.23         6.28        54.77        23.05 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 
       72.20        25.38        19.10         2.66        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1113 TCGA-23-1118 
       31.76        49.41         8.81        29.13        31.20        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-2072 TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 
      129.96         4.27        24.95        87.48        77.00         2.76 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-1104 TCGA-24-1416 TCGA-24-1419 
       11.64        41.56         7.66        63.55         6.38         7.86 
TCGA-24-1425 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 
        5.95        17.39        28.37        43.53        72.92       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
        3.45         1.18        56.58        41.06        51.91        41.39 
TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       88.50        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1846 TCGA-24-1927 
       17.23        90.15        48.33        38.24         4.37        16.44 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       44.84        58.16        14.43        53.95        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2297 TCGA-24-2298 
       44.52        57.07         0.36        31.63        55.86        53.26 
TCGA-25-1315 TCGA-25-1625 TCGA-25-1630 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       51.06        18.02         7.86        13.02        49.05         1.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 TCGA-29-1690 TCGA-29-1694 
       12.00        19.99         2.96        26.99        44.71        38.53 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1702 TCGA-29-1711 TCGA-29-1762 TCGA-29-1768 
        0.79        33.70        18.67        34.62        85.68        31.23 
TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 
       22.55        11.84        12.30         8.38        34.62        62.47 
TCGA-29-2432 TCGA-29-2434 TCGA-30-1857 TCGA-30-1860 TCGA-30-1880 TCGA-30-1891 
       11.84        11.47         0.26        44.91        57.57        30.05 
TCGA-31-1946 TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 
       30.18         6.71        44.12        28.77        21.53        22.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 
       25.74        27.85        35.05        33.01        29.49        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2549 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-57-1584 
        6.05        26.04         9.44        42.02         7.46        21.14 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 
      180.20        80.12        22.32        34.39         5.42        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
       20.94        31.43        28.47        48.79        35.80         2.43 
TCGA-61-1895 TCGA-61-1901 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1995 
        1.45        11.41        31.30        37.05        48.92         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 
        5.52        14.50        17.98        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 TCGA-WR-A838 
       58.39        20.68        44.52       125.75        31.07         8.05 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.30               0.26 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            152.02             180.20 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             24.64              30.84 
[1] "0.3 - 152.0 (24.6)" "0.3 - 180.2 (30.8)"
[1] "hr=" "1.3"
D37V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20Q GAIN MUTATED         2   316                1
  20Q GAIN WILD-TYPE       0   241                1
D37V3, multiclass
                  clus
vv                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  OMENTUM                         2                  0
  OVARY                         316                241
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, continuous
D37V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     2 322
  20Q GAIN WILD-TYPE   1 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      2  322
  20Q GAIN WILD-TYPE    1  246
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 2                  1
  YES              322                246
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED    6 12  4  2
  20Q GAIN WILD-TYPE  8 14  1  1
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0                6                  8
  R1               12                 14
  R2                4                  1
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  2     4
  20Q GAIN WILD-TYPE                                1    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q GAIN MUTATED                          20
  20Q GAIN WILD-TYPE                        12
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           1   277
  20Q GAIN WILD-TYPE                                         0   198
D37V7, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  1
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                               20                 12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  277                198
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     4 180
  20Q GAIN WILD-TYPE   6 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4  180
  20Q GAIN WILD-TYPE    6  145
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              180                145
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    53  51
  21Q GAIN WILD-TYPE 213 239
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               104                452 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                51                239 
$`21Q GAIN MUTATED`
TCGA-04-1332 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1349 TCGA-04-1361 
       41.00        18.51        11.87        65.52        21.57        32.52 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-09-0365 
       82.39        56.55        41.59        19.99        29.10         9.47 
TCGA-09-0366 TCGA-09-1670 TCGA-09-2043 TCGA-10-0928 TCGA-10-0936 TCGA-13-0724 
       57.76        17.98         6.18        18.51        35.80         2.73 
TCGA-13-0726 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 TCGA-13-0888 TCGA-13-0890 
       31.10        32.25         8.45        19.59        70.39        67.99 
TCGA-13-0904 TCGA-13-0911 TCGA-13-1408 TCGA-13-1410 TCGA-13-1496 TCGA-13-1499 
       48.33        27.72         5.92         4.70         4.24        38.40 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-2059 TCGA-20-0990 TCGA-20-0991 
       16.57         4.21         4.41        12.23        25.94        26.20 
TCGA-20-1683 TCGA-23-1021 TCGA-23-1110 TCGA-23-1116 TCGA-23-1119 TCGA-23-1121 
       25.38        47.54        54.51         4.57       129.96         6.38 
TCGA-23-2078 TCGA-23-2643 TCGA-24-0979 TCGA-24-1104 TCGA-24-1424 TCGA-24-1427 
       87.48         4.70        41.56        63.55         6.02         4.83 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1474 TCGA-24-1552 TCGA-24-1558 
        8.55        12.46        45.14        22.22        41.39        19.53 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 TCGA-24-1923 TCGA-24-1928 
        8.32         3.48         3.72        11.28        22.68        11.05 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2260 TCGA-24-2280 TCGA-24-2295 TCGA-25-1312 
        4.87       152.02        36.16        70.45        33.11         1.02 
TCGA-25-1319 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 
       65.00        12.00         2.96        18.58        15.81        20.61 
TCGA-25-1877 TCGA-25-2393 TCGA-25-2401 TCGA-29-1698 TCGA-29-1701 TCGA-29-1707 
       18.05        38.04         2.96        68.32        16.90        41.98 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1778 TCGA-29-2428 TCGA-30-1861 
       85.68        62.93        39.12        14.93        45.11        34.78 
TCGA-30-1862 TCGA-30-1867 TCGA-31-1959 TCGA-36-1571 TCGA-36-1578 TCGA-36-2529 
        6.12         1.22         2.20        22.85        27.85        35.05 
TCGA-36-2542 TCGA-36-2551 TCGA-57-1585 TCGA-61-1722 TCGA-61-1743 TCGA-61-1906 
       21.60        16.18         1.74         8.09        43.69        34.13 
TCGA-61-1907 TCGA-61-1914 TCGA-61-1915 TCGA-61-2003 TCGA-61-2101 TCGA-61-2102 
       31.30        56.61        67.76         4.01        55.50         6.48 
TCGA-61-2111 TCGA-61-2614 
      125.75         8.61 

$`21Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1347 
       40.24         1.81        49.15         2.01        46.62        63.09 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 
       48.76        63.98        65.46        49.28        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
       76.57        71.47        38.37       119.08        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       47.70        45.37        29.16        17.98        35.57         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       38.43        89.33        74.93        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       55.36        30.51         5.85         3.02         8.55        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.12        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       39.75        20.94        26.93        12.46        54.31        25.91 
TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       81.47        33.24        32.28        11.70         3.91        35.44 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       15.12        19.86         6.21        24.59        44.55        39.58 
TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       12.39        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 
       11.38        11.54        34.06        31.04        21.40        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       36.72        28.70        30.35         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        43.86        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 
       68.94       107.18        91.40        74.27        66.67        61.84 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       69.01        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 
       47.38        47.84        44.94        44.84        37.08        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       29.98        21.17        14.89        13.81         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 
        6.08        10.88         6.61         7.36         6.05         6.84 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        54.64        87.06        61.71        29.42 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       98.04        20.68        22.39        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 
       73.55        38.20        49.25        54.31        37.61        13.97 
TCGA-13-1501 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       32.84         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       14.24         8.61        10.78         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
        8.42        23.05        72.20        27.52        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.93         2.66        42.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       31.76        49.41         8.81        29.13        18.90         2.24 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 
       51.35         3.22        31.20        68.68        33.30        86.01 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        4.27        39.09        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 
      115.89        91.66        77.00        49.84         2.76         4.50 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 
        7.63        19.66        11.64        21.80         7.66        22.32 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       54.12        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 
        7.86         0.76         6.25         5.95         5.36        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 
       28.37        19.17        18.67        43.53        72.92       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        9.11         3.45         1.18        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        41.06        51.91        58.09        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       70.62        39.88        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       10.26        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 
        3.81         4.37         5.79         5.52         9.80        30.21 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
       16.44        81.11        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       14.43        53.95        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 
       57.07         0.79         0.36        47.54        31.63        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 
        0.82        67.36        36.23        16.64        55.86        53.26 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        32.02        51.06        37.02         1.02        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 
       36.95        33.96         2.99        18.02         0.36         7.86 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        56.94        60.59        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 
       24.99        85.05        13.02        49.05         1.02         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 
       12.00        45.01        19.99        42.02        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       26.99        78.90        44.71        47.18       101.79        38.53 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 
        0.79        33.70        31.20         0.53        18.67        59.67 
TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1768 
       18.25        29.23        34.62        17.00        66.81        31.23 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       22.98        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       12.30         8.38         7.23         5.36        34.62        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       65.00        62.47         4.90        42.25        11.84        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
        9.76        21.04        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 TCGA-30-1880 
       15.68         0.26        48.10        44.91        36.62        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 
       22.49         6.71        42.51        44.12        28.77        29.10 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 
       21.53        22.55         8.55        30.08        25.74        24.23 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.69        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       23.80         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
        6.05        11.47         7.99        26.04        23.74         9.44 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       42.02         7.46        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       21.14        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
        5.42        44.81        20.52        11.11        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 
       44.84        35.80         2.43        33.67         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 
        5.79        11.41        13.02         9.07        37.05        42.51 
TCGA-61-1913 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       48.92        43.43        15.75        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       14.50        17.98        30.64        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2104 TCGA-61-2109 
       61.64        58.39        60.62        65.52        76.87        20.68 
TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q 
       44.52        22.22         6.35        31.07        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.02               0.26 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            152.02             180.20 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            21.910             29.065 
[1] "1.0 - 152.0 (21.9)" "0.3 - 180.2 (29.1)"
[1] "hr=" "1"  
D38V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  21Q GAIN MUTATED         0   104                2
  21Q GAIN WILD-TYPE       2   453                0
D38V3, multiclass
                  clus
vv                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  OMENTUM                         0                  2
  OVARY                         104                453
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V4, continuous
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0 109
  21Q GAIN WILD-TYPE   3 459
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0  109
  21Q GAIN WILD-TYPE    3  459
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                  3
  YES              109                459
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  21Q GAIN MUTATED    1  6  0  0
  21Q GAIN WILD-TYPE 13 20  5  3
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                1                 13
  R1                6                 20
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     2
  21Q GAIN WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q GAIN MUTATED                           4
  21Q GAIN WILD-TYPE                        28
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           0    93
  21Q GAIN WILD-TYPE                                         1   382
D38V7, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                4                 28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   93                382
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     2  56
  21Q GAIN WILD-TYPE   8 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2   56
  21Q GAIN WILD-TYPE    8  269
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               56                269
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    13  10
  22Q GAIN WILD-TYPE 253 280
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                533 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                10                280 
$`22Q GAIN MUTATED`
TCGA-13-0760 TCGA-13-0762 TCGA-13-1405 TCGA-13-1488 TCGA-23-1119 TCGA-23-2077 
       11.54        32.25         7.36        70.82       129.96       115.89 
TCGA-24-1463 TCGA-24-1469 TCGA-24-1556 TCGA-24-1928 TCGA-24-2290 TCGA-25-1627 
       72.92         9.11        70.62        11.05        36.23         0.36 
TCGA-29-1699 TCGA-29-1764 TCGA-29-1770 TCGA-29-1777 TCGA-29-2425 TCGA-29-2427 
        0.53        62.93        24.36        12.30        65.00        62.47 
TCGA-30-1861 TCGA-31-1950 TCGA-36-2547 TCGA-57-1585 TCGA-61-1904 
       34.78        18.77        20.52         1.74         9.07 

$`22Q GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       63.98        65.46        49.28        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       76.57        71.47        82.39        56.55        41.59        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       38.37       119.08        29.10        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       45.37        29.16         9.47        57.76        17.98        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
        9.99        38.43        89.33        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       61.87        55.36        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        8.55        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
      112.41        71.11        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        54.31        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       32.28        11.70         3.91        35.44        35.80        15.12 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       19.86         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
       12.39        31.10        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.18        11.38        34.06        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       38.93        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        7.79         8.12         8.28         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       66.67        70.39        61.84        67.99        69.01        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       57.47        56.15        57.07        19.36        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       29.98        21.17        14.89        13.81         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
        6.08        10.88         6.61         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
        4.70         4.21         5.33        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 
       29.42        98.04        20.68        22.39        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       73.55        38.20        49.25         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       38.40        13.97        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
        4.77         4.18         2.56         3.91         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       12.23         8.61        10.78         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.42        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       42.54        40.54        15.39        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        8.81        29.13        18.90         2.24        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
        3.22        31.20        68.68         4.57        33.30        86.01 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
        4.27         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       24.95        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.70         4.50         7.63        19.66        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 
       28.37        19.17        18.67        43.53         8.55        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14       105.99         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       41.39        58.09        88.50        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       88.37        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.81         4.37        11.28         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       22.68        30.21        16.44        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
        0.82        67.36        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        32.02        51.06        37.02         1.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        36.95        33.96         2.99        12.00 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 
        2.96        18.58        18.02        15.81        20.61         7.86 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        56.94        60.59        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       24.99        18.05        85.05        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       38.04         3.02        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        44.71 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       47.18       101.79        38.53         0.79        33.70        31.20 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       68.32        16.90        18.67        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 
       29.23        34.62        17.00        85.68        66.81        39.12 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       31.23        22.98        22.55        17.33        12.36        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        34.62        86.17 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       45.11         4.90        42.25        11.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       21.04        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
        0.26        48.10        44.91         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       22.49         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       25.74        27.85        24.23        24.69        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
        2.24        20.98        18.31        14.17         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       11.47         7.99        26.04        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
        7.46        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       44.81        20.52        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       44.84        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 
        8.42         5.79        11.41        13.02        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
        4.01        30.64        39.85        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       58.39        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       20.68        44.52       125.75        22.22         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        8.61        39.68        18.94         0.79         8.05 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.36               0.26 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            129.96             180.20 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             24.36              28.18 
[1] "0.4 - 130.0 (24.4)" "0.3 - 180.2 (28.2)"
[1] "hr=" "1.6"
D39V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  22Q GAIN MUTATED         1    23                0
  22Q GAIN WILD-TYPE       1   534                2
D39V3, multiclass
                  clus
vv                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  OMENTUM                         1                  1
  OVARY                          23                534
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, continuous
D39V5, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  24
  22Q GAIN WILD-TYPE   3 544
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   24
  22Q GAIN WILD-TYPE    3  544
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                  3
  YES               24                544
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  22Q GAIN MUTATED    1  2  0  0
  22Q GAIN WILD-TYPE 13 24  5  3
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                1                 13
  R1                2                 24
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q GAIN MUTATED                           0
  22Q GAIN WILD-TYPE                        32
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    22
  22Q GAIN WILD-TYPE                                         1   453
D39V7, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    0                 18
  BLACK OR AFRICAN AMERICAN                                0                 32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   22                453
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  12
  22Q GAIN WILD-TYPE  10 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   12
  22Q GAIN WILD-TYPE   10  313
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 10
  NOT HISPANIC OR LATINO               12                313
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    49  56
  XQ GAIN WILD-TYPE 217 234
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              105               451 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               56               234 
$`XQ GAIN MUTATED`
TCGA-04-1342 TCGA-04-1346 TCGA-04-1351 TCGA-04-1525 TCGA-04-1652 TCGA-04-1655 
       18.51        65.52        65.46        38.37        31.86        45.37 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-10-0927 TCGA-10-0933 
        8.55         6.18        35.15         4.54        81.47        11.70 
TCGA-10-0936 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0726 TCGA-13-0727 
       35.80        24.59        44.55        39.58        31.10        15.19 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0761 TCGA-13-0768 TCGA-13-0795 TCGA-13-0797 
       55.17        11.18        34.06         8.45        19.59         8.71 
TCGA-13-0800 TCGA-13-0804 TCGA-13-0884 TCGA-13-0890 TCGA-13-0897 TCGA-13-0901 
        8.12        35.28       107.18        67.99        57.47        19.36 
TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-1404 TCGA-13-1409 TCGA-13-1485 
       21.17         4.64         6.41         6.61         6.84        20.68 
TCGA-13-1488 TCGA-13-1504 TCGA-13-1505 TCGA-13-2057 TCGA-13-2060 TCGA-13-2065 
       70.82        16.57         4.21        14.24         8.61         8.75 
TCGA-13-2071 TCGA-20-0987 TCGA-20-0991 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
        6.28        23.05        26.20        16.70         2.93         2.66 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1809 TCGA-23-2077 
       51.35        54.51         3.22        68.68         0.53       115.89 
TCGA-23-2084 TCGA-24-1104 TCGA-24-1474 TCGA-24-1556 TCGA-24-1563 TCGA-24-1564 
       49.84        63.55        22.22        70.62        47.70        25.87 
TCGA-24-1604 TCGA-24-1843 TCGA-24-1846 TCGA-24-1924 TCGA-24-2038 TCGA-24-2261 
       88.37         3.48         4.37        30.21        44.52         0.79 
TCGA-24-2281 TCGA-25-1319 TCGA-25-1320 TCGA-25-1329 TCGA-25-1632 TCGA-25-1633 
       44.61        65.00        36.95         2.96        56.94        60.59 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2397 TCGA-25-2398 TCGA-29-1691 TCGA-29-1699 
       24.99        18.05        12.00        45.01        47.18         0.53 
TCGA-29-1710 TCGA-29-1764 TCGA-29-1766 TCGA-29-1776 TCGA-29-1778 TCGA-29-A5NZ 
       29.23        62.93        39.12        11.84        14.93        21.04 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1862 TCGA-30-1867 TCGA-31-1951 TCGA-36-2529 
       51.91         2.47         6.12         1.22        22.49        35.05 
TCGA-57-1584 TCGA-57-1586 TCGA-59-2348 TCGA-59-2372 TCGA-61-1722 TCGA-61-1741 
       21.14        22.32       180.20        44.81         8.09        33.67 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1911 TCGA-61-1915 TCGA-61-2087 TCGA-61-2109 
        8.42         5.79        42.51        67.76         4.80        20.68 
TCGA-61-2612 TCGA-61-2614 TCGA-VG-A8LO 
        6.35         8.61         0.79 

$`XQ GAIN WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       11.87        63.09        48.76        21.57        63.98        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       32.52        44.32        33.67        76.57        71.47        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       56.55        41.59        19.99       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       47.70        29.16         9.47        57.76        17.98        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
        9.99        38.43        89.33        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       61.87        55.36        30.51        17.98         5.85         3.02 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       97.55         6.12       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 
       20.94        26.93        12.46        54.31        25.91        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       33.24        32.28         3.91        35.44        15.12        19.86 
TCGA-13-0714 TCGA-13-0724 TCGA-13-0725 TCGA-13-0730 TCGA-13-0755 TCGA-13-0758 
        6.21         2.73        12.39        17.82         2.50        11.38 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 
       11.54        32.25        31.04        21.40        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       28.70        30.35         7.79         8.28         8.19        43.86 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       35.28        13.61        68.94        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 
       70.39        61.84        69.01        43.36        56.15        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 
       27.72        34.06        29.98        14.89        13.81         6.08 
TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 
       10.88         7.36         6.05         5.92         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       22.39        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
        4.24        54.31        37.61        38.40        13.97        32.84 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.41         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2059 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0996 
       12.23        10.78        54.77         8.42        25.94        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       27.52        25.38        19.10        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       18.90         2.24        31.20         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
      129.96         4.27         6.38        39.09        33.47        58.13 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 
       24.95        87.48        91.66        77.00         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
        7.66        22.32        54.12        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        5.95         5.36         4.83        17.39        28.37        19.17 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 
      105.99         9.11         3.45         1.18        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       58.09        88.50        39.88        19.53        44.09        45.50 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       10.26        17.23        90.15        48.33        38.24         8.32 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.72         3.81        11.28         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       22.68        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 
       18.48        28.18        64.01        57.07        36.16         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       47.54        31.63        70.45         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       16.64        33.11        55.86        53.26         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 
       32.02        51.06        37.02         1.02        34.98        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
        2.99        12.00        18.58        18.02        15.81         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
       20.61         7.86         0.30        35.54        51.22        14.96 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       85.05        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        44.71       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32        16.90        18.67        59.67        18.25 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1768 
       41.98        34.62        17.00        85.68        66.81        31.23 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 
       22.98        24.36        22.55        17.33        12.36        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
        8.38         7.23         5.36        34.62        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       62.47        45.11         4.90        42.25        11.84        11.47 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
        9.76        38.07        36.26        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
       44.91        34.78        36.62        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 
       48.79        45.57        30.18        18.77         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       44.12         2.20        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.55         8.55        30.08        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.69        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       23.80        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 
       14.17         6.05        16.18        11.47         7.99        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74         9.44        42.02         7.46        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       24.03        11.38         1.74        29.00        25.08        25.02 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        5.42        20.52        11.11        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1901 TCGA-61-1903 
       35.80         2.43        43.69         1.45        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 
        9.07        34.13        31.30        37.05        48.92        56.61 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       43.43        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       17.98         4.01        30.64        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96        45.40         4.77        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       58.39        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q 
       44.52       125.75        22.22        31.07        39.68        18.94 
TCGA-WR-A838 
        8.05 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.53              0.26 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           180.20            152.02 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            22.32             29.00 
[1] "0.5 - 180.2 (22.3)" "0.3 - 152.0 (29.0)"
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  XQ GAIN MUTATED         0   103                2
  XQ GAIN WILD-TYPE       2   454                0
D40V3, multiclass
                  clus
vv                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  OMENTUM                        0                 2
  OVARY                        103               454
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V4, continuous
D40V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0 105
  XQ GAIN WILD-TYPE   3 463
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0  105
  XQ GAIN WILD-TYPE    3  463
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                0                 3
  YES             105               463
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  XQ GAIN MUTATED    1  3  1  0
  XQ GAIN WILD-TYPE 13 23  4  3
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               1                13
  R1               3                23
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     2
  XQ GAIN WILD-TYPE                                3    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ GAIN MUTATED                           7
  XQ GAIN WILD-TYPE                        25
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           0    91
  XQ GAIN WILD-TYPE                                         1   384
D40V7, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               7                25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  91               384
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     2  69
  XQ GAIN WILD-TYPE   8 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2   69
  XQ GAIN WILD-TYPE    8  256
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              69               256
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    29  31
  1P LOSS WILD-TYPE 237 259
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               60               496 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               31               259 
$`1P LOSS MUTATED`
TCGA-04-1351 TCGA-04-1362 TCGA-04-1514 TCGA-04-1542 TCGA-04-1638 TCGA-09-1669 
       65.46        44.32        56.55        84.20        55.43        30.51 
TCGA-09-1672 TCGA-09-2056 TCGA-10-0928 TCGA-10-0935 TCGA-13-0761 TCGA-13-0762 
        5.85        12.46        18.51        35.44        34.06        32.25 
TCGA-13-0794 TCGA-13-0905 TCGA-13-1409 TCGA-13-1477 TCGA-13-1484 TCGA-13-1489 
       30.35        47.84         6.84        54.64        98.04        82.88 
TCGA-13-1497 TCGA-13-2065 TCGA-20-1682 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
       54.31         8.75        27.52         2.93         2.66        42.54 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1423 
        4.70         4.50        22.32        54.12        47.41         6.25 
TCGA-24-1424 TCGA-24-1850 TCGA-24-2020 TCGA-25-1316 TCGA-25-1877 TCGA-25-2396 
        6.02         5.52       152.02        37.02        18.05         3.02 
TCGA-25-2408 TCGA-29-1690 TCGA-29-1705 TCGA-29-1763 TCGA-29-1768 TCGA-29-2429 
       31.00        44.71        18.25        66.81        31.23         4.90 
TCGA-30-1853 TCGA-30-1859 TCGA-30-1860 TCGA-36-1569 TCGA-36-1576 TCGA-36-1580 
       36.26        48.10        44.91        29.10        30.08        24.23 
TCGA-36-2540 TCGA-36-2543 TCGA-36-2552 TCGA-57-1585 TCGA-59-2352 TCGA-59-A5PD 
       23.80         2.24        11.47         1.74         9.40        20.52 
TCGA-61-1727 TCGA-61-1918 TCGA-61-2012 TCGA-61-2101 TCGA-61-2612 TCGA-WR-A838 
       18.54        15.75        30.64        55.50         6.35         8.05 

$`1P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       63.98        49.28        32.52        33.67        76.57        71.47 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       82.39        41.59        19.99        38.37       119.08        29.10 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       47.70        45.37        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       35.57         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 
       57.60        61.87        55.36        17.98         3.02         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       97.55         6.18         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-10-0925 
       71.11        63.09        39.75        20.94        26.93        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       25.91        81.47        33.24        32.28        11.70         3.91 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.80        15.12        19.86         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       39.58         2.73        12.39        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 
       55.17         2.50        11.18        11.38        11.54        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       21.40         8.45        38.93        36.72        28.70        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
        8.71         7.79         8.12         8.28         8.19        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       35.28        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       74.27        66.67        70.39        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       48.33        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       29.98        21.17        14.89        13.81         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.08        10.88         6.61         7.36         6.05         5.92 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.70         4.21         5.33        87.06        61.71        29.42 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       20.68        22.39        70.82        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       49.25         4.24        37.61        38.40        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       16.57         4.21         4.41         4.77         4.18         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
        3.91         3.09        14.24        12.23         8.61        10.78 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        6.28        54.77         8.42        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1023 
       72.20        25.38        19.10        16.70        47.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       18.90         2.24        51.35        54.51         3.22        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       68.68         4.57        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        6.38        39.09        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        11.64        21.80        41.56         7.66 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       63.55         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        0.76         5.95         5.36         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       19.17        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       45.14       105.99         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        3.48         3.72         3.81         4.37        11.28         5.79 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
        4.87        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       53.95        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       55.86        53.26         1.02        26.96        32.02        51.06 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        1.02        34.98        65.00        36.95        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       12.00         2.96        18.58        18.02        15.81         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       51.22        14.96        24.99        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
        1.02        38.04        12.00        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 
        2.96        29.03        26.99        78.90        47.18       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       38.53         0.79        33.70        31.20        68.32         0.53 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       16.90        18.67        59.67        41.98        29.23        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 
       17.00        85.68        62.93        39.12        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.55        17.33        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
        8.38         7.23         5.36        34.62        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       62.47        45.11        42.25        11.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       21.04        38.07        51.91         2.47        15.68         0.26 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 
        6.71        42.51        44.12         2.20        28.77        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 
       22.85        22.55         8.55        25.74        27.85        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
       21.60        20.98        18.31        20.52        14.17         6.05 
TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       16.18         7.99        26.04        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
        7.46        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       22.32       116.12        34.39         2.14         5.42        44.81 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 
       11.11         8.09        20.94        31.43        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       31.79        28.47        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       33.67        43.69         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       13.02         9.07        34.13        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 
       48.92        56.61        67.76        43.43        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        5.52        14.50        17.98         4.01        30.64        39.85 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
        1.18        45.96        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 
       71.74        61.64        58.39        60.62        65.52         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 
       76.87        20.68        44.52       125.75        22.22        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        8.61        39.68        18.94         0.79 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1.74              0.26 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           152.02            180.20 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            29.59             27.88 
[1] "1.7 - 152.0 (29.6)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1P LOSS MUTATED         0    63                0
  1P LOSS WILD-TYPE       2   494                2
D41V3, multiclass
                  clus
vv                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         63               494
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, continuous
D41V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     1  63
  1P LOSS WILD-TYPE   2 505
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   63
  1P LOSS WILD-TYPE    2  505
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                1                 2
  YES              63               505
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED    1  4  0  0
  1P LOSS WILD-TYPE 13 22  5  3
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0               1                13
  R1               4                22
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P LOSS MUTATED                           6
  1P LOSS WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           0    49
  1P LOSS WILD-TYPE                                         1   426
D41V7, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               6                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  49               426
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2  35
  1P LOSS WILD-TYPE   8 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   35
  1P LOSS WILD-TYPE    8  290
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              35               290
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    17  22
  1Q LOSS WILD-TYPE 249 268
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               39               517 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               268 
$`1Q LOSS MUTATED`
TCGA-04-1351 TCGA-04-1362 TCGA-10-0928 TCGA-13-0761 TCGA-13-0794 TCGA-13-0905 
       65.46        44.32        18.51        34.06        30.35        47.84 
TCGA-13-1407 TCGA-13-1477 TCGA-13-1489 TCGA-13-1497 TCGA-13-2065 TCGA-20-1682 
        6.05        54.64        82.88        54.31         8.75        27.52 
TCGA-23-1022 TCGA-23-1109 TCGA-23-2643 TCGA-23-2645 TCGA-24-1103 TCGA-24-1105 
       42.54        51.35         4.70         4.50        54.12        47.41 
TCGA-24-1424 TCGA-24-1850 TCGA-24-2020 TCGA-25-1877 TCGA-25-2408 TCGA-29-1705 
        6.02         5.52       152.02        18.05        31.00        18.25 
TCGA-29-1763 TCGA-29-1768 TCGA-29-2429 TCGA-30-1853 TCGA-30-1859 TCGA-30-1860 
       66.81        31.23         4.90        36.26        48.10        44.91 
TCGA-36-1580 TCGA-36-2543 TCGA-57-1585 TCGA-59-2352 TCGA-59-A5PD TCGA-61-1727 
       24.23         2.24         1.74         9.40        20.52        18.54 
TCGA-61-2012 TCGA-61-2612 TCGA-WR-A838 
       30.64         6.35         8.05 

$`1Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       63.98        49.28        32.52        33.67        76.57        71.47 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        41.59        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       29.10        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 
       64.64        36.23        31.86        47.70        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
        9.47        57.76        17.98        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       89.33        74.93        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       30.51        17.98         5.85         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        6.18         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       63.09        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       25.91        81.47        33.24        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       35.44        35.80        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       44.55        39.58         2.73        12.39        31.10        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       17.82        55.17         2.50        11.18        11.38        11.54 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       32.25        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       28.70        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.19        43.86        35.28        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
      107.18        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       67.99        69.01        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36        47.38        48.33        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 
        5.92         6.84         4.70         4.21         5.33        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       61.71        29.42        98.04        20.68        22.39        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 
       52.44        73.55        38.20        49.25         4.24        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       38.40        13.97        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
        4.77         4.18         2.56         3.91         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
       12.23         8.61        10.78         6.28        54.77         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
       23.05        25.94        26.20        72.20        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 
       16.70         2.93         2.66        47.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        31.76        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        2.24        54.51         3.22        31.20        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       33.30        86.01       129.96         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       33.47        58.13         0.53        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0968 
       91.66        77.00        49.84         2.76         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 
       11.64        21.80        41.56         7.66        22.32        63.55 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        6.25         5.95         5.36         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       19.17        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       45.14       105.99         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        3.48         3.72         3.81         4.37        11.28         5.79 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
        4.87        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       53.95        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       36.16         0.79         0.36        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       55.86        53.26         1.02        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
        2.99        12.00         2.96        18.58        18.02        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
        0.36        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 
       35.54        51.22        14.96        24.99        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       49.05         1.02        38.04         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 
       19.99        42.02         2.96        29.03        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       44.71        47.18       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       31.20        68.32         0.53        16.90        18.67        59.67 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 
       41.98        29.23        34.62        17.00        85.68        62.93 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       39.12        22.98        24.36        22.55        17.33        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       11.84        12.30        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 
       34.62        86.17        65.00        62.47        45.11        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       11.84        11.47         9.76        21.04        38.07        51.91 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 
        2.47        15.68         0.26        34.78         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
        2.20        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 
        8.55        30.08        25.74        27.85        24.69        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       33.01        29.49        29.82        25.91        25.08        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
       21.60        20.98        18.31        20.52        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       16.18        11.47         7.99        26.04        23.74         9.44 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       42.02         7.46        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       21.14        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       80.12        22.32       116.12        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 
       44.81        11.11         8.09        20.94        31.43        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
        4.34        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
        2.43        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       42.51        48.92        56.61        67.76        43.43        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       30.64        39.85         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        4.77        51.72        71.74        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       65.52        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75        22.22        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO 
        0.79 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.74              0.26 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           152.02            180.20 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            30.35             27.88 
[1] "1.7 - 152.0 (30.4)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1.1"
D42V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  1Q LOSS MUTATED         0    42                0
  1Q LOSS WILD-TYPE       2   515                2
D42V3, multiclass
                  clus
vv                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         42               515
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V4, continuous
D42V5, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  42
  1Q LOSS WILD-TYPE   2 526
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   42
  1Q LOSS WILD-TYPE    2  526
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                1                 2
  YES              42               526
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  1Q LOSS MUTATED    0  3  0  0
  1Q LOSS WILD-TYPE 14 23  5  3
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               0                14
  R1               3                23
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q LOSS MUTATED                           5
  1Q LOSS WILD-TYPE                        27
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0    31
  1Q LOSS WILD-TYPE                                         1   444
D42V7, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               5                27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  31               444
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  23
  1Q LOSS WILD-TYPE   9 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   23
  1Q LOSS WILD-TYPE    9  302
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              23               302
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    22  30
  2P LOSS WILD-TYPE 244 260
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               52               504 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               30               260 
$`2P LOSS MUTATED`
TCGA-04-1343 TCGA-04-1349 TCGA-04-1362 TCGA-04-1514 TCGA-04-1517 TCGA-04-1536 
       11.87        21.57        44.32        56.55        19.99        29.10 
TCGA-09-1673 TCGA-13-0723 TCGA-13-0751 TCGA-13-0762 TCGA-13-0883 TCGA-13-0890 
        3.02        39.58        55.17        32.25        68.94        67.99 
TCGA-13-0891 TCGA-13-0904 TCGA-13-0916 TCGA-13-0924 TCGA-13-1411 TCGA-13-1484 
       69.01        48.33        21.17         6.08         4.21        98.04 
TCGA-13-1494 TCGA-13-1507 TCGA-20-0991 TCGA-20-1682 TCGA-23-1116 TCGA-24-1413 
       38.20         4.77        26.20        27.52         4.57         6.31 
TCGA-24-1464 TCGA-24-1563 TCGA-24-1614 TCGA-24-1847 TCGA-24-1923 TCGA-24-1930 
       12.46        47.70        48.33        11.28        22.68        81.11 
TCGA-24-2020 TCGA-24-2260 TCGA-24-2280 TCGA-25-1313 TCGA-25-1318 TCGA-25-1321 
      152.02        36.16        70.45        26.96        34.98        33.96 
TCGA-25-1627 TCGA-25-1878 TCGA-25-2392 TCGA-29-1688 TCGA-29-1693 TCGA-29-1699 
        0.36        85.05         1.02        78.90       101.79         0.53 
TCGA-29-1761 TCGA-29-1770 TCGA-30-1853 TCGA-36-2543 TCGA-36-2545 TCGA-61-1743 
       17.00        24.36        36.26         2.24        18.31        43.69 
TCGA-61-2016 TCGA-61-2087 TCGA-61-2092 TCGA-61-2109 
        1.18         4.80        51.72        20.68 

$`2P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 
       18.51        65.52        63.09        48.76        63.98        65.46 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       49.28        32.52        33.67        76.57        71.47        82.39 
TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       41.59        38.37       119.08        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       45.37        29.16         9.47        57.76        17.98        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
        9.99        38.43        89.33        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 
       61.87        55.36        30.51        17.98         5.85         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
       97.55         6.18         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 
       71.11        63.09        39.75        20.94        26.93        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       54.31        25.91        81.47        18.51        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       11.70         3.91        35.44        35.80        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
        6.21        24.59        44.55         2.73        12.39        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       15.19        17.82         2.50        11.18        11.38        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       34.06        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       28.70        30.35        19.59         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        43.86        35.28        35.28        13.61 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
      107.18        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 
       29.98        14.89        13.81         4.64         6.41        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.61         7.36         6.05         5.92         6.84         4.70 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 
        5.33        54.64        87.06        61.71        29.42        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 
       22.39        70.82        82.88        52.44        73.55        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
        4.24        54.31        37.61        38.40        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       16.57         4.21         4.41         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        3.09        14.24        12.23         8.61        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 
        6.28        54.77         8.42        23.05        25.94        72.20 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       42.54        40.54        15.39        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        8.81        29.13        18.90         2.24        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
        3.22        31.20        68.68        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
        4.27         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       24.95       115.89        87.48        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
        2.76         4.70         4.50         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       21.80        41.56         7.66        22.32        54.12        63.55 
TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
       47.41         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       28.37        19.17        18.67        43.53         8.55        72.92 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       45.14       105.99         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       26.96        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       19.53        44.09        45.50        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       90.15        88.37        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 
        3.81         4.37         5.79         5.52         9.80        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       16.44        11.05         4.87        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
      109.71        14.43        53.95        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       44.52        57.07         0.79         0.36        47.54        31.63 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26         1.02        32.02        51.06        37.02 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
        1.02        65.00        36.95         2.99        12.00         2.96 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.58        18.02        15.81        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       56.94        60.59        35.54        51.22        14.96        24.99 
TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       18.05        13.02        49.05        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       26.99        44.71        47.18        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32        16.90        18.67        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       41.98        29.23        34.62        85.68        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       39.12        31.23        22.98        22.55        17.33        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       11.84        12.30        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       34.62        86.17        65.00        62.47        45.11         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        11.84        11.47         9.76        21.04        38.07 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       51.91         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
        6.71        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       27.85        24.23        24.69        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 
       29.82        25.91        25.08        23.80        21.60        20.98 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       20.52        14.17         6.05        16.18        11.47         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       26.04        23.74         9.44        42.02         7.46        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        1.48        24.03        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       29.00        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      116.12         9.40        34.39         2.14         5.42        44.81 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       20.52        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       35.80         2.43        33.67         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
       11.41        13.02         9.07        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       42.51        48.92        56.61        67.76        43.43        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       38.17         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 
       30.64        39.85        30.64        45.96        45.40         4.77 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
        6.48        76.87        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61        39.68        18.94         0.79         8.05 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.36              0.26 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           152.02            180.20 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            28.31             28.03 
[1] "0.4 - 152.0 (28.3)" "0.3 - 180.2 (28.0)"
[1] "hr=" "1.1"
D43V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  2P LOSS MUTATED         0    53                0
  2P LOSS WILD-TYPE       2   504                2
D43V3, multiclass
                  clus
vv                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         53               504
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V4, continuous
D43V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  53
  2P LOSS WILD-TYPE   3 515
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   53
  2P LOSS WILD-TYPE    3  515
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                0                 3
  YES              53               515
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  2P LOSS MUTATED    1  1  0  0
  2P LOSS WILD-TYPE 13 25  5  3
D43V6, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                46 
       TCGA-04-1516        TCGA-04-1644        TCGA-13-0807        TCGA-13-0911 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-13-A5FT        TCGA-13-A5FU        TCGA-24-2033        TCGA-29-2414 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-29-2425        TCGA-29-2427        TCGA-29-2428        TCGA-29-2429 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-29-2431        TCGA-29-2432        TCGA-29-2434        TCGA-29-2436 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-36-2529        TCGA-36-2530        TCGA-36-2532        TCGA-36-2534 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-36-2537        TCGA-36-2538        TCGA-36-2540        TCGA-36-2542 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-36-2544        TCGA-36-2547        TCGA-36-2548        TCGA-36-2549 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-36-2551        TCGA-36-2552        TCGA-3P-A9WA        TCGA-42-2582 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-42-2587        TCGA-42-2588        TCGA-42-2589        TCGA-42-2590 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-42-2593        TCGA-57-1993        TCGA-59-2363        TCGA-59-2372 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-61-2612        TCGA-61-2613        TCGA-61-2614        TCGA-OY-A56P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-OY-A56Q        TCGA-VG-A8LO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     1
  2P LOSS WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED                           2
  2P LOSS WILD-TYPE                        30
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           0    47
  2P LOSS WILD-TYPE                                         1   428
D43V7, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               2                30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  47               428
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  31
  2P LOSS WILD-TYPE  10 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   31
  2P LOSS WILD-TYPE   10  294
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              31               294
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    27  30
  2Q LOSS WILD-TYPE 239 260
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               57               499 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               30               260 
$`2Q LOSS MUTATED`
TCGA-04-1336 TCGA-04-1342 TCGA-04-1349 TCGA-04-1517 TCGA-09-1673 TCGA-13-0723 
       49.15        18.51        21.57        19.99         3.02        39.58 
TCGA-13-0751 TCGA-13-0762 TCGA-13-0890 TCGA-13-0891 TCGA-13-0904 TCGA-13-0916 
       55.17        32.25        67.99        69.01        48.33        21.17 
TCGA-13-0924 TCGA-13-1411 TCGA-13-1484 TCGA-13-1494 TCGA-13-1507 TCGA-13-A5FU 
        6.08         4.21        98.04        38.20         4.77         8.42 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1686 TCGA-23-1116 TCGA-24-1413 TCGA-24-1464 
       26.20        27.52         2.93         4.57         6.31        12.46 
TCGA-24-1563 TCGA-24-1614 TCGA-24-1847 TCGA-24-1923 TCGA-24-1930 TCGA-24-2020 
       47.70        48.33        11.28        22.68        81.11       152.02 
TCGA-24-2029 TCGA-24-2260 TCGA-24-2280 TCGA-25-1313 TCGA-25-1318 TCGA-25-1627 
       14.43        36.16        70.45        26.96        34.98         0.36 
TCGA-25-1635 TCGA-25-2392 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1699 
       51.22         1.02        26.99        78.90       101.79         0.53 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1761 TCGA-29-1770 TCGA-29-1774 TCGA-30-1853 
       16.90        18.67        17.00        24.36        17.33        36.26 
TCGA-30-1887 TCGA-36-1575 TCGA-36-2529 TCGA-36-2543 TCGA-36-2545 TCGA-61-2016 
       24.26         8.55        35.05         2.24        18.31         1.18 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2109 
        4.80        51.72        20.68 

$`2Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       40.24        41.00         1.81         2.01        46.62        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       65.52        63.09        48.76        63.98        65.46        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       32.52        44.32        33.67        76.57        71.47        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       56.55        41.59        38.37       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       31.86        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       17.98        35.57         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       41.62        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        5.85         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        4.54       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       33.24        32.28        11.70         3.91        35.44        35.80 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 
       15.12        19.86         6.21        24.59        44.55         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 
       12.39        31.10        15.19        17.82         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.38        11.54        34.06        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       38.93        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        7.79         8.12         8.28         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       66.67        70.39        61.84        43.36        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       57.07        19.36        47.38        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 
       37.08        27.72        34.06        29.98        14.89        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        4.64         6.41        10.88         6.61         7.36         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        5.92         6.84         4.70         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       61.71        29.42        20.68        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       52.44        73.55        49.25         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       38.40        13.97        32.84        16.57         4.21         4.41 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.18         2.56         3.91         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 
        8.61        10.78         8.75         6.28        54.77        23.05 
TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 
       25.94        72.20        25.38        19.10        16.70         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        42.54        40.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       49.41         8.81        29.13        18.90         2.24        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 
       54.51         3.22        31.20        68.68        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
      129.96         4.27         6.38        39.09        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        0.53        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 
       49.84         2.76         4.70         4.50         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       11.64        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       63.55        47.41         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        19.17        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        45.14       105.99         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 
       39.88        19.53        44.09        45.50        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
       17.23        90.15        88.37        38.24         8.32         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.72         3.81         4.37         5.79         5.52         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 
       30.21        16.44        11.05         4.87        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       34.82       109.71        53.95        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       44.52        57.07         0.79         0.36        47.54        31.63 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       44.61         0.82        67.36        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26         1.02        32.02        51.06        37.02 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
        1.02        65.00        36.95        33.96         2.99        12.00 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 
        2.96        18.58        18.02        15.81        20.61         7.86 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
        0.30        56.94        60.59        35.54        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 
       18.05        85.05        13.02        49.05        38.04         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
       12.00        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       31.00        44.71        47.18        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       31.20        68.32        59.67        18.25        41.98        29.23 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       34.62        85.68        66.81        62.93        39.12        31.23 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       22.98        22.55        12.36        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
        8.38         7.23         5.36        34.62        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       62.47        45.11         4.90        42.25        11.84        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
        9.76        21.04        38.07        51.91         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 
        0.26        48.10        44.91        34.78         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
        1.22        57.57        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       18.77        22.49         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 
       28.77        29.10        21.53        22.85        22.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 
       25.74        27.85        24.23        24.69        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 
       29.82        25.91        25.08        23.80        21.60        20.98 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       20.52        14.17         6.05        16.18        11.47         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       26.04        23.74         9.44        42.02         7.46        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        1.48        24.03        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       29.00        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
      116.12         9.40        34.39         2.14         5.42        44.81 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       20.52        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       35.80         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 
        4.01        30.64        39.85        30.64        45.96        45.40 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
        4.77        71.74        61.64        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07         8.61        39.68        18.94         0.79 
TCGA-WR-A838 
        8.05 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.36              0.26 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           152.02            180.20 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            22.68             29.00 
[1] "0.4 - 152.0 (22.7)" "0.3 - 180.2 (29.0)"
[1] "hr=" "1"  
D44V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  2Q LOSS MUTATED         0    57                1
  2Q LOSS WILD-TYPE       2   500                1
D44V3, multiclass
                  clus
vv                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         57               500
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, continuous
D44V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  59
  2Q LOSS WILD-TYPE   3 509
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   59
  2Q LOSS WILD-TYPE    3  509
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                0                 3
  YES              59               509
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  2Q LOSS MUTATED    1  2  1  0
  2Q LOSS WILD-TYPE 13 24  4  3
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               1                13
  R1               2                24
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     1
  2Q LOSS WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q LOSS MUTATED                           2
  2Q LOSS WILD-TYPE                        30
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           0    50
  2Q LOSS WILD-TYPE                                         1   425
D44V7, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               2                30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  50               425
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  30
  2Q LOSS WILD-TYPE  10 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   30
  2Q LOSS WILD-TYPE   10  295
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              30               295
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    44  48
  3P LOSS WILD-TYPE 222 242
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               92               464 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               48               242 
$`3P LOSS MUTATED`
TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 TCGA-04-1356 TCGA-04-1365 TCGA-04-1514 
       65.52        63.09        65.46        49.28        76.57        56.55 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1652 TCGA-09-0369 TCGA-09-1667 
       38.37       119.08        84.20        31.86        35.57        61.87 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-10-0938 TCGA-13-0730 TCGA-13-0757 
       71.11        63.09        39.75        19.86        17.82        11.18 
TCGA-13-0792 TCGA-13-0794 TCGA-13-0890 TCGA-13-0920 TCGA-13-1407 TCGA-13-1408 
       36.72        30.35        67.99        13.81         6.05         5.92 
TCGA-13-1409 TCGA-13-1411 TCGA-13-1487 TCGA-13-1492 TCGA-13-1499 TCGA-13-1512 
        6.84         4.21        22.39        73.55        38.40         3.09 
TCGA-13-2057 TCGA-13-2060 TCGA-20-0990 TCGA-23-1024 TCGA-23-1031 TCGA-23-1032 
       14.24         8.61        25.94        15.39        18.90         2.24 
TCGA-23-1114 TCGA-24-0968 TCGA-24-0970 TCGA-24-1417 TCGA-24-1418 TCGA-24-1464 
       68.68        19.66        11.64         7.82         7.99        12.46 
TCGA-24-1469 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1846 TCGA-24-1930 
        9.11        57.40        16.21        41.06         4.37        81.11 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2262 TCGA-24-2288 TCGA-24-2293 TCGA-25-1312 
       34.82       109.71         0.36         0.82        16.64         1.02 
TCGA-25-1317 TCGA-25-1320 TCGA-25-1323 TCGA-25-1627 TCGA-25-1633 TCGA-25-1870 
        1.02        36.95        12.00         0.36        60.59        14.96 
TCGA-25-2392 TCGA-25-2397 TCGA-29-1691 TCGA-29-1693 TCGA-29-1699 TCGA-29-1763 
        1.02        12.00        47.18       101.79         0.53        66.81 
TCGA-29-1764 TCGA-29-1777 TCGA-30-1855 TCGA-30-1887 TCGA-31-1959 TCGA-36-1575 
       62.93        12.30         2.47        24.26         2.20         8.55 
TCGA-36-1576 TCGA-36-1580 TCGA-36-2530 TCGA-36-2552 TCGA-42-2589 TCGA-42-2593 
       30.08        24.23        33.01        11.47        42.02         1.48 
TCGA-57-1992 TCGA-59-2363 TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 TCGA-61-1741 
       29.00         5.42         8.09         4.34        31.79        33.67 
TCGA-61-1743 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 TCGA-61-2012 TCGA-61-2016 
       43.69        56.61        43.43        38.17        30.64         1.18 
TCGA-61-2104 TCGA-61-2113 
       76.87        22.22 

$`3P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1361 
       18.51        11.87        48.76        21.57        63.98        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 
       44.32        33.67        71.47        82.39        41.59        19.99 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       29.10        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       36.23        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       17.98         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       57.60        55.36        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        8.55        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
      112.41        20.94        26.93        12.46        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       81.47        18.51        33.24        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        35.80        15.12         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 
       39.58         2.73        12.39        31.10        15.19        55.17 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
        2.50        11.38        11.54        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
       21.40         8.45        38.93        28.70        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        7.79         8.12         8.28         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       66.67        70.39        61.84        69.01        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       56.15        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        14.89         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.61         7.36         4.70         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 
       61.71        29.42        98.04        20.68        70.82        82.88 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       52.44        38.20        49.25         4.24        54.31        37.61 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       13.97        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
        4.18         2.56         3.91        12.23        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 
        6.28        54.77         8.42        23.05        26.20        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        42.54        40.54        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
        8.81        29.13        51.35        54.51         3.22        31.20 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
        4.57        33.30        86.01       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
       39.09        33.47        58.13         0.53        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       87.48        91.66        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        4.50         7.63        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 
       54.12        63.55        47.41         6.31         6.38         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
       17.39        28.37        19.17        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       72.92        45.14       105.99         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1546 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       26.96        64.27        56.58        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       47.70        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       48.33        38.24         8.32         3.48         3.72         3.81 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 
       11.28         5.79         5.52         9.80        22.68        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       16.44        11.05         4.87       152.02        44.84        58.16 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       14.43        53.95        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       57.07        36.16         0.79        47.54        31.63        70.45 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       44.61        67.36        36.23        33.11        55.86        53.26 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 
       26.96        32.02        51.06        37.02        34.98        65.00 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       33.96         2.99         2.96        18.58        18.02        15.81 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 
       20.61         7.86         0.30        56.94        35.54        51.22 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 
       24.99        18.05        85.05        13.02        49.05        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
        3.02        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 
       31.00        26.99        78.90        44.71        38.53         0.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.70        31.20        68.32        16.90        18.67        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        29.23        34.62        17.00        85.68 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.12        31.23        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        11.84        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       34.62        86.17        65.00        62.47        45.11         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        11.84        11.47         9.76        21.04        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       51.91        36.26        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 
       34.78         6.12        36.62         1.22        57.57        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       42.51        44.12        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2532 
       22.55        25.74        27.85        24.69        35.05        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.82        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       20.98        18.31        20.52        14.17         6.05        16.18 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 
        7.99        26.04        23.74         9.44         7.46        40.77 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 
       24.03        11.38        21.14         1.74        22.32        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.02       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 
       34.39         2.14        44.81        20.52        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       31.43        18.54        27.88        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       35.80         2.43         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       13.02         9.07        34.13        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       48.92        67.76        15.75         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2017 TCGA-61-2018 
       17.98         4.01        30.64        39.85        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 
       60.62        65.52        55.50         6.48        20.68        44.52 
TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.36              0.26 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           119.08            180.20 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           24.245            28.420 
[1] "0.4 - 119.1 (24.2)" "0.3 - 180.2 (28.4)"
[1] "hr=" "1"  
D45V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3P LOSS MUTATED         1    92                0
  3P LOSS WILD-TYPE       1   465                2
D45V3, multiclass
                  clus
vv                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  OMENTUM                        1                 1
  OVARY                         92               465
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, continuous
D45V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  92
  3P LOSS WILD-TYPE   2 476
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   92
  3P LOSS WILD-TYPE    2  476
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                1                 2
  YES              92               476
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  3P LOSS MUTATED    3  1  1  0
  3P LOSS WILD-TYPE 11 25  4  3
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               3                11
  R1               1                25
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  1     2
  3P LOSS WILD-TYPE                                2    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED                           2
  3P LOSS WILD-TYPE                        30
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           0    80
  3P LOSS WILD-TYPE                                         1   395
D45V7, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   2                16
  BLACK OR AFRICAN AMERICAN                               2                30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  80               395
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  55
  3P LOSS WILD-TYPE   9 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   55
  3P LOSS WILD-TYPE    9  270
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              55               270
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    20  22
  3Q LOSS WILD-TYPE 246 268
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               42               514 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               22               268 
$`3Q LOSS MUTATED`
TCGA-04-1351 TCGA-04-1356 TCGA-04-1514 TCGA-04-1652 TCGA-09-2050 TCGA-10-0938 
       65.46        49.28        56.55        31.86        71.11        19.86 
TCGA-13-0730 TCGA-13-0762 TCGA-13-0794 TCGA-13-0890 TCGA-13-1407 TCGA-13-1408 
       17.82        32.25        30.35        67.99         6.05         5.92 
TCGA-13-1492 TCGA-13-1499 TCGA-13-1512 TCGA-23-1024 TCGA-23-1032 TCGA-24-0968 
       73.55        38.40         3.09        15.39         2.24        19.66 
TCGA-24-1418 TCGA-24-1469 TCGA-24-1545 TCGA-24-1550 TCGA-24-2262 TCGA-24-2288 
        7.99         9.11        57.40        41.06         0.36         0.82 
TCGA-24-2293 TCGA-25-1320 TCGA-25-2392 TCGA-25-2397 TCGA-29-1691 TCGA-29-1699 
       16.64        36.95         1.02        12.00        47.18         0.53 
TCGA-29-1763 TCGA-29-1777 TCGA-30-1855 TCGA-31-1959 TCGA-36-1575 TCGA-36-1580 
       66.81        12.30         2.47         2.20         8.55        24.23 
TCGA-42-2589 TCGA-57-1992 TCGA-61-1730 TCGA-61-1741 TCGA-61-1743 TCGA-61-2012 
       42.02        29.00         4.34        33.67        43.69        30.64 

$`3Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       63.98        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       82.39        41.59        19.99        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       84.20        55.43        48.89        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       36.23        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       17.98        35.57         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       41.62        57.60        61.87        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
       35.15         4.54       112.41        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       33.24        32.28        11.70         3.91        35.44        35.80 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       15.12         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       12.39        31.10        15.19        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.38        11.54        34.06        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       38.93        36.72        28.70        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
        8.12         8.28         8.19        43.86        35.28        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       70.39        61.84        69.01        43.36        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       14.89        13.81         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.61         7.36         6.84         4.70         4.21         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       54.64        87.06        61.71        29.42        98.04        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 
       22.39        70.82        82.88        52.44        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
        4.24        54.31        37.61        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.21         4.41         4.77         4.18         2.56         3.91 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
       14.24        12.23         8.61        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       54.77         8.42        23.05        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        42.54        40.54        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
        8.81        29.13        18.90        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       31.20        68.68         4.57        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
        4.27         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       24.95       115.89        87.48        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
        2.76         4.70         4.50         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.31         6.38         7.82         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        6.02         5.95         5.36         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       19.17        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14       105.99         3.45         1.18        22.22        26.96 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       64.27        16.21        56.58        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       47.70        25.87        10.26        17.23        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       48.33        38.24         8.32         3.48         3.72         3.81 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
       30.21        16.44        11.05        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 
        0.79        47.54        31.63        70.45        44.61        67.36 
TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       36.23        33.11        55.86        53.26         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       32.02        51.06        37.02         1.02        34.98        65.00 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       33.96         2.99        12.00         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       15.81         0.36        20.61         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       60.59        35.54        51.22        14.96        24.99        18.05 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       85.05        13.02        49.05        38.04         3.02        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        44.71       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32        16.90        18.67        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 
       41.98        29.23        34.62        17.00        85.68        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.12        31.23        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        11.84        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       34.62        86.17        65.00        62.47        45.11         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        11.84        11.47         9.76        21.04        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       51.91        36.26        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
        6.71        42.51        44.12        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 
       22.85        22.55        30.08        25.74        27.85        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       23.80        21.60         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 
       14.17         6.05        16.18        11.47         7.99        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       23.74         9.44         7.46        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 
       11.38        21.14         1.74        22.32        25.08        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
      180.20        80.12        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 
        2.14         5.42        44.81        20.52        11.11         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 
       20.94        31.43        18.54        27.88        31.79        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 
       48.79        44.84        35.80         2.43         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       15.75        38.17         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        4.01        30.64        39.85         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        4.80         4.77        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       39.68        18.94         0.79         8.05 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.36              0.26 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            73.55            180.20 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           22.045            28.275 
[1] "0.4 - 73.5 (22.0)"  "0.3 - 180.2 (28.3)"
[1] "hr=" "1.3"
D46V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  3Q LOSS MUTATED         1    42                0
  3Q LOSS WILD-TYPE       1   515                2
D46V3, multiclass
                  clus
vv                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  OMENTUM                        1                 1
  OVARY                         42               515
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, continuous
D46V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  42
  3Q LOSS WILD-TYPE   2 526
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   42
  3Q LOSS WILD-TYPE    2  526
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                1                 2
  YES              42               526
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  3Q LOSS MUTATED    1  0  0  0
  3Q LOSS WILD-TYPE 13 26  5  3
D46V6, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                47 
       TCGA-04-1516        TCGA-04-1644        TCGA-13-0807        TCGA-13-0911 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-13-A5FT        TCGA-13-A5FU        TCGA-24-2033        TCGA-29-2414 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-29-2425        TCGA-29-2427        TCGA-29-2428        TCGA-29-2429 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-29-2431        TCGA-29-2432        TCGA-29-2434        TCGA-29-2436 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-36-2529        TCGA-36-2530        TCGA-36-2532        TCGA-36-2534 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-36-2537        TCGA-36-2538        TCGA-36-2540        TCGA-36-2542 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-36-2543        TCGA-36-2544        TCGA-36-2545        TCGA-36-2547 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-36-2548        TCGA-36-2549        TCGA-36-2551        TCGA-36-2552 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-3P-A9WA        TCGA-42-2582        TCGA-42-2587        TCGA-42-2588 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-42-2590        TCGA-42-2593        TCGA-57-1993        TCGA-59-2363 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-59-2372        TCGA-61-2612        TCGA-61-2613        TCGA-61-2614 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-OY-A56P        TCGA-OY-A56Q        TCGA-VG-A8LO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                3    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED                           2
  3Q LOSS WILD-TYPE                        30
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           0    37
  3Q LOSS WILD-TYPE                                         1   438
D46V7, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   0                18
  BLACK OR AFRICAN AMERICAN                               2                30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  37               438
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  24
  3Q LOSS WILD-TYPE   9 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   24
  3Q LOSS WILD-TYPE    9  301
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              24               301
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   140 159
  4P LOSS WILD-TYPE 126 131
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              299               257 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              159               131 
$`4P LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 
       40.24        41.00        46.62        11.87        48.76        63.98 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       32.52        44.32        82.39        56.55        41.59        19.99 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 TCGA-04-1651 
       29.10        84.20        55.43        48.89        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 
       31.86        47.70        45.37         9.47        17.98        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 
        9.99        38.43        89.33        61.87        30.51        17.98 
TCGA-09-1673 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        3.02         6.18         6.12       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       39.75        20.94        81.47        18.51        33.24        32.28 
TCGA-10-0933 TCGA-10-0935 TCGA-13-0717 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 
       11.70        35.44        24.59        12.39        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 
       55.17         2.50        11.18        11.54        32.25        31.04 
TCGA-13-0766 TCGA-13-0793 TCGA-13-0795 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
       21.40        28.70        19.59         8.28        43.86        35.28 
TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       35.28       107.18        91.40        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0910 
       67.99        56.15        57.07        47.38        48.33        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 
       27.72        34.06        14.89         4.64         6.08        10.88 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 
        6.05         5.92         6.84         4.70         4.21        87.06 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       98.04        22.39        70.82        82.88        52.44        73.55 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 TCGA-13-1509 
       49.25        54.31        37.61        13.97        16.57         4.18 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
        3.91         3.09        12.23        10.78         8.75        54.77 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 
       25.94        26.20        27.52        25.38        19.10         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
        2.66        47.54        42.54        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 
       18.90         2.24         3.22        31.20         4.57        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2084 
       86.01       129.96        39.09        33.47        24.95        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        2.76         4.70        19.66        11.64        21.80        41.56 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       22.32        54.12        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 TCGA-24-1426 TCGA-24-1431 TCGA-24-1434 
        7.99         0.76         5.95         5.36        19.17        18.67 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
        8.55        72.92         9.11         3.45         1.18        22.22 
TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 
       16.21        51.91        41.39        88.50        44.09        45.50 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 
       17.23        90.15        88.37        38.24         8.32         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 
        3.81         4.37        11.28         5.52        22.68        30.21 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 
       81.11         4.87       152.02        44.84       109.71        14.43 
TCGA-24-2030 TCGA-24-2254 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       53.95        57.07         0.79        47.54        31.63        70.45 
TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
        0.82        36.23        16.64        33.11        55.86        53.26 
TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 
       32.02        37.02         1.02        34.98        36.95        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.99        12.00        18.58        15.81         0.36        20.61 
TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-2400 
        0.30        60.59        35.54        14.96        24.99        42.02 
TCGA-25-2404 TCGA-29-1688 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       29.03        78.90         0.79        31.20        68.32         0.53 
TCGA-29-1701 TCGA-29-1705 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1771 
       16.90        18.25        85.68        62.93        31.23        22.55 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 
       12.30        14.93         8.38         7.23         5.36        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 
       65.00        45.11        42.25        11.47        38.07        36.26 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1891 
       15.68        48.10        34.78        36.62        57.57        30.05 
TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1576 
       18.77         6.71        42.51         2.20        28.77        30.08 
TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2532 TCGA-36-2538 TCGA-36-2542 
       25.74        24.23        24.69        29.49        25.08        21.60 
TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 
        2.24        18.31        14.17        16.18        11.47        23.74 
TCGA-42-2588 TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 
        9.44        40.77        24.03        21.14         1.74        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       25.08        25.02        22.32         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 
        5.42        44.81        20.52         4.34        28.47        48.79 
TCGA-61-1737 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 
       44.84        33.67         1.45         8.42         5.79        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 
        9.07        34.13        48.92        56.61        43.43        38.17 
TCGA-61-1995 TCGA-61-2003 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
        2.01         4.01         1.18        45.40         4.80        51.72 
TCGA-61-2094 TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       71.74        55.50         6.48        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07        39.68        18.94 

$`4P LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 
        1.81        49.15         2.01        18.51        65.52        63.09 
TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       21.57        65.46        49.28        33.67        76.57        71.47 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1646 TCGA-04-1648 TCGA-09-0364 TCGA-09-0366 
       38.37       119.08        27.88        28.64        29.16        57.76 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1672 TCGA-09-1674 
       74.93        41.62        57.60        55.36         5.85         8.55 
TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       97.55        35.15         4.54        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       25.91         3.91        35.80        15.12        19.86         6.21 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0758 TCGA-13-0761 
       44.55        39.58         2.73        31.10        11.38        34.06 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
        8.45        38.93        36.72        30.35         8.71         7.79 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0891 
        8.12         8.19        13.61        68.94        74.27        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       43.36        57.47        19.36        47.84        44.94        44.84 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-1404 TCGA-13-1405 
       29.98        21.17        13.81         6.41         6.61         7.36 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1494 
        5.33        54.64        61.71        29.42        20.68        38.20 
TCGA-13-1496 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
        4.24        38.40        32.84         4.21         4.41         4.77 
TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0987 
        2.56        14.24         8.61         6.28         8.42        23.05 
TCGA-20-0996 TCGA-20-1685 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       72.20        16.70        40.54        15.39        26.83        31.76 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 
       51.35        54.51        68.68         4.27         6.38        58.13 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2645 
        0.53       115.89        87.48        91.66        77.00         4.50 
TCGA-24-0966 TCGA-24-0980 TCGA-24-1104 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 
        7.63         7.66        63.55         7.86         6.25         6.02 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 TCGA-24-1464 TCGA-24-1466 
        4.83        17.39        28.37        43.53        12.46        45.14 
TCGA-24-1467 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 
      105.99        26.96        57.40        64.27        56.58        41.06 
TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 
       58.09        70.62        39.88        19.53        47.70        25.87 
TCGA-24-1565 TCGA-24-1614 TCGA-24-1843 TCGA-24-1849 TCGA-24-1920 TCGA-24-1927 
       10.26        48.33         3.48         5.79         9.80        16.44 
TCGA-24-1928 TCGA-24-2024 TCGA-24-2026 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       11.05        58.16        34.82        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2281 TCGA-24-2289 TCGA-25-1312 
       44.52        36.16         0.36        44.61        67.36         1.02 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1319 TCGA-25-1329 TCGA-25-1625 TCGA-25-1630 
       26.96        51.06        65.00         2.96        18.02         7.86 
TCGA-25-1632 TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       56.94        51.22        18.05        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
        1.02        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
        2.96        31.00        26.99        44.71        47.18       101.79 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 
       38.53        33.70        18.67        59.67        41.98        29.23 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 
       34.62        17.00        66.81        39.12        22.98        24.36 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 
       17.33        12.36        11.84        34.62        62.47         4.90 
TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 
       11.84         9.76        21.04        51.91         2.47         0.26 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
       44.91         6.12         1.22        24.26        48.79        45.57 
TCGA-31-1946 TCGA-31-1951 TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       30.18        22.49        44.12        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 TCGA-36-2534 
       22.55         8.55        27.85        35.05        33.01        29.82 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 TCGA-3P-A9WA 
       25.91        23.80        20.98        20.52         6.05         7.99 
TCGA-42-2582 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 TCGA-57-1586 
       26.04        42.02         7.46         1.48        11.38        22.32 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
      180.20        80.12       116.12        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1738 TCGA-61-1740 
       31.43        18.54        27.88        31.79        35.80         2.43 
TCGA-61-1743 TCGA-61-1901 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 
       43.69        11.41        31.30        37.05        42.51        67.76 
TCGA-61-1918 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 
       15.75         5.52        14.50        17.98        30.64        39.85 
TCGA-61-2012 TCGA-61-2017 TCGA-61-2088 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
       30.64        45.96         4.77        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2104 TCGA-61-2614 TCGA-VG-A8LO TCGA-WR-A838 
       65.52        76.87         8.61         0.79         8.05 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.30              0.26 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           152.02            180.20 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            27.72             28.18 
[1] "0.3 - 152.0 (27.7)" "0.3 - 180.2 (28.2)"
[1] "hr=" "1.1"
D47V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  4P LOSS MUTATED         2   301                0
  4P LOSS WILD-TYPE       0   256                2
D47V3, multiclass
                  clus
vv                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  OMENTUM                        2                 0
  OVARY                        301               256
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, continuous
D47V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     2 310
  4P LOSS WILD-TYPE   1 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2  310
  4P LOSS WILD-TYPE    1  258
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                2                 1
  YES             310               258
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED    9 13  2  2
  4P LOSS WILD-TYPE  5 13  3  1
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0               9                 5
  R1              13                13
  R2               2                 3
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  1     8
  4P LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED                          15
  4P LOSS WILD-TYPE                        17
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           1   260
  4P LOSS WILD-TYPE                                         0   215
D47V7, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   8                10
  BLACK OR AFRICAN AMERICAN                              15                17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 260               215
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     5 173
  4P LOSS WILD-TYPE   5 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5  173
  4P LOSS WILD-TYPE    5  152
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 5
  NOT HISPANIC OR LATINO             173               152
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   163 182
  4Q LOSS WILD-TYPE 103 108
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              345               211 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              182               108 
$`4Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 TCGA-04-1348 
       40.24        41.00        49.15        46.62        11.87        48.76 
TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 
       63.98        32.52        44.32        33.67        71.47        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       56.55        41.59        19.99        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       48.89        27.88        64.64        31.86        47.70        45.37 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       17.98        35.57         9.99        38.43        89.33        74.93 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 
       57.60        61.87        30.51        17.98         3.02         8.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.18         6.12       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       20.94        26.93        12.46        25.91        81.47        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0935 TCGA-10-0937 TCGA-13-0717 
       33.24        32.28        11.70        35.44        15.12        24.59 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       44.55         2.73        12.39        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0766 TCGA-13-0793 TCGA-13-0795 
       11.18        11.54        32.25        21.40        28.70        19.59 
TCGA-13-0797 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0884 
        8.71         8.28        43.86        35.28        35.28       107.18 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0899 
       91.40        66.67        70.39        61.84        67.99        56.15 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 
       47.38        48.33        37.08        27.72        34.06        21.17 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 
       14.89         4.64         6.08        10.88         6.61         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 
        5.92         6.84         4.70        87.06        29.42        98.04 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 
       22.39        70.82        82.88        52.44        73.55        49.25 
TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1509 
       54.31        38.40        13.97        16.57         4.21         4.18 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
        3.91         3.09        12.23        10.78         8.75        54.77 
TCGA-20-0990 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.94        25.38        19.10         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       42.54        49.41         8.81        29.13        18.90         2.24 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       54.51         3.22        31.20        68.68         4.57        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2084 
       86.01       129.96        39.09        33.47        24.95        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        2.76         4.70        19.66        11.64        21.80        41.56 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       22.32        54.12        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 
        7.99         7.86         0.76         6.25         5.95         5.36 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1469 
       17.39        19.17        18.67         8.55        72.92         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 
        3.45         1.18        22.22        26.96        57.40        16.21 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       51.91        41.39        88.50        44.09        45.50        47.70 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 
       17.23        90.15        88.37        38.24         8.32         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.81         4.37        11.28         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       22.68        11.05        81.11         4.87       152.02        44.84 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2254 TCGA-24-2261 TCGA-24-2267 
      109.71        14.43        53.95        57.07         0.79        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 
       31.63        70.45        44.61         0.82        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86        53.26         1.02        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       37.02         1.02        34.98        36.95        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       12.00         2.96        18.58        18.02        15.81         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       20.61         7.86         0.30        60.59        35.54        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2398 
       14.96        24.99        13.02        49.05         1.02        45.01 
TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1695 TCGA-29-1697 
       42.02        29.03        31.00        78.90         0.79        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1762 TCGA-29-1764 TCGA-29-1769 
       68.32         0.53        18.25        85.68        62.93        22.98 
TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       22.55        11.84        12.30         8.38         7.23         5.36 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2434 TCGA-30-1714 
       86.17        65.00        45.11        42.25        11.47        38.07 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1859 TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 
       36.26        15.68        48.10        34.78        36.62        57.57 
TCGA-30-1891 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       30.05        30.18        18.77         6.71        42.51         2.20 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 
       28.77        21.53        22.85        30.08        25.74        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2538 TCGA-36-2542 
       24.69        35.05        33.01        29.49        25.08        21.60 
TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
        2.24        18.31        14.17        16.18        11.47         7.99 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74         9.44        42.02         7.46        40.77         1.48 
TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       24.03        21.14         1.74        29.00        25.08        25.02 
TCGA-59-2350 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
       22.32         9.40         2.14         5.42        44.81        20.52 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 
        4.34        31.79        28.47        48.79        44.84        33.67 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        8.42         5.79        13.02         9.07        34.13        31.30 
TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-2003 
       56.61        43.43        15.75        38.17         2.01         4.01 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 
       39.85         1.18        45.40         4.80        51.72        71.74 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       39.68        18.94         0.79 

$`4Q LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 
        1.81         2.01        18.51        65.52        63.09        21.57 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1365 TCGA-04-1525 TCGA-04-1530 TCGA-04-1648 
       65.46        49.28        76.57        38.37       119.08        28.64 
TCGA-04-1651 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-1665 TCGA-09-1668 
       36.23        29.16         9.47        57.76        41.62        55.36 
TCGA-09-1672 TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 TCGA-10-0925 TCGA-10-0934 
        5.85        97.55        35.15         4.54        54.31         3.91 
TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0723 TCGA-13-0726 TCGA-13-0755 
       35.80        19.86         6.21        39.58        31.10         2.50 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       11.38        34.06        31.04         8.45        38.93        36.72 
TCGA-13-0794 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 
       30.35         7.79         8.12         8.19        13.61        68.94 
TCGA-13-0886 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 
       74.27        69.01        43.36        57.47        57.07        19.36 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 TCGA-13-0920 TCGA-13-0923 
       47.84        44.94        44.84        29.98        13.81         6.41 
TCGA-13-1405 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 
        7.36         4.21         5.33        54.64        61.71        20.68 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 TCGA-13-1501 TCGA-13-1506 TCGA-13-1507 
       38.20         4.24        37.61        32.84         4.41         4.77 
TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0987 
        2.56        14.24         8.61         6.28         8.42        23.05 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 TCGA-23-1023 TCGA-23-1024 
       26.20        72.20        27.52        16.70        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1109 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 
       26.83        31.76        51.35         4.27         6.38        58.13 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2645 
        0.53       115.89        87.48        91.66        77.00         4.50 
TCGA-24-0966 TCGA-24-0980 TCGA-24-1104 TCGA-24-1424 TCGA-24-1427 TCGA-24-1430 
        7.63         7.66        63.55         6.02         4.83        28.37 
TCGA-24-1435 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1546 TCGA-24-1549 
       43.53        12.46        45.14       105.99        64.27        56.58 
TCGA-24-1550 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1564 
       41.06        58.09        70.62        39.88        19.53        25.87 
TCGA-24-1565 TCGA-24-1614 TCGA-24-1843 TCGA-24-1924 TCGA-24-1927 TCGA-24-2024 
       10.26        48.33         3.48        30.21        16.44        58.16 
TCGA-24-2026 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 
       34.82        18.48        28.18        64.01        44.52        36.16 
TCGA-24-2262 TCGA-24-2289 TCGA-25-1313 TCGA-25-1319 TCGA-25-1632 TCGA-25-1877 
        0.36        67.36        26.96        65.00        56.94        18.05 
TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 
       85.05        38.04         3.02        12.00        19.99         2.96 
TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       26.99        44.71        47.18       101.79        38.53        33.70 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       16.90        18.67        59.67        41.98        29.23        34.62 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 
       17.00        66.81        39.12        31.23        24.36        17.33 
TCGA-29-1775 TCGA-29-1778 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 
       12.36        14.93        34.62        62.47         4.90        11.84 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 TCGA-30-1860 
        9.76        21.04        51.91         2.47         0.26        44.91 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1951 
        6.12         1.22        24.26        48.79        45.57        22.49 
TCGA-31-1956 TCGA-36-1569 TCGA-36-1574 TCGA-36-1575 TCGA-36-1578 TCGA-36-2534 
       44.12        29.10        22.55         8.55        27.85        29.82 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 TCGA-42-2582 
       25.91        23.80        20.98        20.52         6.05        26.04 
TCGA-57-1583 TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2354 
       11.38        22.32       180.20        80.12       116.12        34.39 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       11.11         8.09        20.94        31.43        18.54        27.88 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1901 TCGA-61-1910 
       35.80         2.43        43.69         1.45        11.41        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       42.51        48.92        67.76         5.52        14.50        17.98 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2017 TCGA-61-2088 TCGA-61-2095 TCGA-61-2096 
       30.64        30.64        45.96         4.77        61.64        58.39 
TCGA-WR-A838 
        8.05 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.30              0.26 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           152.02            180.20 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            26.93             29.10 
[1] "0.3 - 152.0 (26.9)" "0.3 - 180.2 (29.1)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  4Q LOSS MUTATED         2   346                1
  4Q LOSS WILD-TYPE       0   211                1
D48V3, multiclass
                  clus
vv                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  OMENTUM                        2                 0
  OVARY                        346               211
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, continuous
D48V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     2 356
  4Q LOSS WILD-TYPE   1 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2  356
  4Q LOSS WILD-TYPE    1  212
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                2                 1
  YES             356               212
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   10 17  4  3
  4Q LOSS WILD-TYPE  4  9  1  0
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              10                 4
  R1              17                 9
  R2               4                 1
  RX               3                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  3     9
  4Q LOSS WILD-TYPE                                0     9
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED                          20
  4Q LOSS WILD-TYPE                        12
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           1   296
  4Q LOSS WILD-TYPE                                         0   179
D48V7, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        3                 0
  ASIAN                                                   9                 9
  BLACK OR AFRICAN AMERICAN                              20                12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 296               179
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     8 195
  4Q LOSS WILD-TYPE   2 130
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8  195
  4Q LOSS WILD-TYPE    2  130
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                 2
  NOT HISPANIC OR LATINO             195               130
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    59  69
  5P LOSS WILD-TYPE 207 221
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              128               428 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               69               221 
$`5P LOSS MUTATED`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1338 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       41.00        49.15        46.62        65.46        49.28        32.52 
TCGA-04-1371 TCGA-04-1517 TCGA-04-1648 TCGA-09-0364 TCGA-09-0365 TCGA-09-1669 
       82.39        19.99        28.64        29.16         9.47        30.51 
TCGA-09-2044 TCGA-09-2049 TCGA-10-0938 TCGA-13-0714 TCGA-13-0724 TCGA-13-0761 
        6.12       112.41        19.86         6.21         2.73        34.06 
TCGA-13-0762 TCGA-13-0791 TCGA-13-0795 TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 
       32.25        38.93        19.59         8.12        43.86        35.28 
TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 
       35.28       107.18        91.40        66.67        70.39        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0919 TCGA-13-0920 TCGA-13-1405 TCGA-13-1412 
       69.01        43.36        14.89        13.81         7.36         5.33 
TCGA-13-1491 TCGA-13-1496 TCGA-13-1497 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       52.44         4.24        54.31        14.24        12.23         8.61 
TCGA-20-1682 TCGA-20-1683 TCGA-23-1021 TCGA-23-1022 TCGA-23-1028 TCGA-23-1109 
       27.52        25.38        47.54        42.54        49.41        51.35 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-24-0970 
       68.68        86.01        39.09        33.47        24.95        11.64 
TCGA-24-1419 TCGA-24-1424 TCGA-24-1430 TCGA-24-1431 TCGA-24-1464 TCGA-24-1466 
        7.86         6.02        28.37        19.17        12.46        45.14 
TCGA-24-1548 TCGA-24-1558 TCGA-24-1567 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 
       16.21        19.53        17.23        48.33         8.32         3.48 
TCGA-24-1920 TCGA-24-2019 TCGA-24-2035 TCGA-24-2254 TCGA-24-2261 TCGA-24-2271 
        9.80         4.87        28.18        57.07         0.79        31.63 
TCGA-24-2293 TCGA-25-1312 TCGA-25-1313 TCGA-25-1317 TCGA-25-1320 TCGA-25-1323 
       16.64         1.02        26.96         1.02        36.95        12.00 
TCGA-25-1630 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2398 
        7.86        60.59        51.22        14.96        24.99        45.01 
TCGA-25-2400 TCGA-29-1697 TCGA-29-1702 TCGA-29-1711 TCGA-29-1762 TCGA-29-1778 
       42.02        31.20        18.67        34.62        85.68        14.93 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2428 TCGA-30-1855 TCGA-30-1859 
        7.23         5.36        86.17        45.11         2.47        48.10 
TCGA-30-1861 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-31-1953 TCGA-31-1959 
       34.78         1.22        24.26        30.05         6.71         2.20 
TCGA-36-1575 TCGA-36-2538 TCGA-36-2547 TCGA-36-2552 TCGA-3P-A9WA TCGA-57-1583 
        8.55        25.08        20.52        11.47         7.99        11.38 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-61-1724 
       25.02       180.20       116.12         9.40         5.42        20.94 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1741 TCGA-61-1743 TCGA-61-1906 TCGA-61-1907 
       27.88         4.34        33.67        43.69        34.13        31.30 
TCGA-61-1917 TCGA-61-1998 TCGA-61-2094 TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 
       43.43         5.52        71.74        60.62         6.48        76.87 
TCGA-OY-A56Q TCGA-WR-A838 
       18.94         8.05 

$`5P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       40.24         1.81         2.01        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1362 TCGA-04-1364 
       63.09        48.76        21.57        63.98        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 
       76.57        71.47        56.55        41.59        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 
       29.10        84.20        55.43        48.89        27.88        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-0367 
       36.23        31.86        47.70        45.37        57.76        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       35.57         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       57.60        61.87        55.36        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
        8.55        97.55         6.18        35.15         4.54        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       63.09        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.47        18.51        33.24        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0717 TCGA-13-0720 
        3.91        35.44        35.80        15.12        24.59        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58        12.39        31.10        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 TCGA-13-0766 
        2.50        11.18        11.38        11.54        31.04        21.40 
TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
        8.45        36.72        28.70        30.35         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 
        8.28         8.19        13.61        68.94        74.27        61.84 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       57.47        56.15        57.07        19.36        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       29.98        21.17         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        6.61         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       54.64        87.06        61.71        29.42        98.04        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       22.39        70.82        82.88        73.55        38.20        49.25 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       37.61        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.41         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       10.78         8.75         6.28        54.77         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       25.94        26.20        72.20        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 
        2.66        40.54        15.39        26.83        31.76         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       29.13        18.90         2.24        54.51         3.22        31.20 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 
        4.57        33.30       129.96         4.27         6.38        58.13 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
        0.53       115.89        87.48        91.66        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0975 
        2.76         4.70         4.50         7.63        19.66        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 
        6.31         6.38         7.82         7.99         0.76         6.25 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 
        5.95         5.36         4.83        17.39        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
        8.55        72.92       105.99         9.11         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 
       22.22        26.96        57.40        64.27        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 
       44.09        45.50        47.70        25.87        10.26        90.15 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       88.37        38.24         3.72         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.79         5.52        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
       81.11       152.02        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 
       14.43        53.95        18.48        64.01        44.52        36.16 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
        0.36        47.54        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 TCGA-25-1315 
       36.23        33.11        55.86        53.26        32.02        51.06 
TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 
       37.02        34.98        65.00        33.96         2.99         2.96 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
       18.58        18.02        15.81         0.36        20.61         0.30 
TCGA-25-1632 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       56.94        35.54        18.05        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 
        1.02        38.04         3.02        12.00        19.99         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
       29.03        31.00        26.99        78.90        44.71        47.18 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 
      101.79        38.53         0.79        33.70        68.32         0.53 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 
       16.90        59.67        18.25        41.98        29.23        17.00 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       66.81        62.93        39.12        31.23        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       22.55        17.33        12.36        11.84        12.30         8.38 
TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       34.62        65.00        62.47         4.90        42.25        11.84 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       11.47         9.76        21.04        38.07        51.91        36.26 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1880 
       15.68         0.26        44.91         6.12        36.62        57.57 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 
       48.79        45.57        30.18        18.77        22.49        42.51 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       44.12        28.77        29.10        21.53        22.85        22.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
       30.08        25.74        27.85        24.23        24.69        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 
       33.01        29.49        29.82        25.91        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
        2.24        20.98        18.31        14.17         6.05        16.18 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       26.04        23.74         9.44        42.02         7.46        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
        1.48        24.03        21.14         1.74        22.32        29.00 
TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 
       25.08        80.12        22.32        34.39         2.14        44.81 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1733 
       20.52        11.11         8.09        31.43        18.54        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 
       28.47        48.79        44.84        35.80         2.43         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1910 
        8.42         5.79        11.41        13.02         9.07        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 
       42.51        48.92        56.61        67.76        15.75        38.17 
TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        2.01        14.50        17.98         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2109 
       51.72        61.64        58.39        65.52        55.50        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-VG-A8LO 
       39.68         0.79 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.79              0.26 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           180.20            152.02 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           27.700            28.585 
[1] "0.8 - 180.2 (27.7)" "0.3 - 152.0 (28.6)"
[1] "hr=" "1"  
D49V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  5P LOSS MUTATED         1   129                0
  5P LOSS WILD-TYPE       1   428                2
D49V3, multiclass
                  clus
vv                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  OMENTUM                        1                 1
  OVARY                        129               428
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, continuous
D49V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0 131
  5P LOSS WILD-TYPE   3 437
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0  131
  5P LOSS WILD-TYPE    3  437
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                0                 3
  YES             131               437
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  5P LOSS MUTATED    3  3  0  2
  5P LOSS WILD-TYPE 11 23  5  1
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               3                11
  R1               3                23
  R2               0                 5
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     5
  5P LOSS WILD-TYPE                                3    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P LOSS MUTATED                           6
  5P LOSS WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           0   112
  5P LOSS WILD-TYPE                                         1   363
D49V7, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   5                13
  BLACK OR AFRICAN AMERICAN                               6                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 112               363
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  76
  5P LOSS WILD-TYPE   7 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   76
  5P LOSS WILD-TYPE    7  249
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO              76               249
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   105 108
  5Q LOSS WILD-TYPE 161 182
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              213               343 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              108               182 
$`5Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1338 TCGA-04-1350 TCGA-04-1351 
       40.24        41.00        49.15        46.62        63.98        65.46 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1371 TCGA-04-1517 TCGA-04-1646 TCGA-04-1648 
       49.28        32.52        82.39        19.99        27.88        28.64 
TCGA-04-1649 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-1669 TCGA-09-1674 
       64.64        29.16         9.47        57.76        30.51         8.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2054 TCGA-10-0927 TCGA-10-0938 
        6.18         6.12       112.41        20.94        81.47        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0730 TCGA-13-0760 
        6.21        24.59        39.58         2.73        17.82        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 
       34.06        32.25        31.04        21.40        38.93        28.70 
TCGA-13-0794 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       30.35         8.12         8.28         8.19        43.86        35.28 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 
      107.18        91.40        66.67        70.39        67.99        69.01 
TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0906 TCGA-13-0916 
       43.36        56.15        19.36        48.33        44.94        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 TCGA-13-1412 
       14.89        13.81         7.36         6.05         4.21         5.33 
TCGA-13-1484 TCGA-13-1491 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1505 
       98.04        52.44         4.24        54.31        38.40         4.21 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       14.24        12.23         8.61        25.94        26.20        27.52 
TCGA-20-1684 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1026 TCGA-23-1028 
       19.10         2.93        47.54        42.54        26.83        49.41 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 
       29.13        18.90         2.24        51.35        54.51        31.20 
TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 
       68.68        86.01       129.96        39.09        33.47        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2643 TCGA-24-0970 TCGA-24-1419 TCGA-24-1424 
       24.95       115.89         4.70        11.64         7.86         6.02 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
       28.37        19.17        12.46        45.14       105.99         9.11 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1558 TCGA-24-1564 TCGA-24-1567 TCGA-24-1614 
       16.21        56.58        19.53        25.87        17.23        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1924 TCGA-24-1928 TCGA-24-2019 
       38.24         8.32         3.48        30.21        11.05         4.87 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 
      152.02        34.82        53.95        28.18        57.07        36.16 
TCGA-24-2261 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2293 TCGA-24-2295 
        0.79        31.63        70.45        44.61        16.64        33.11 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 
        1.02        26.96        51.06         1.02        34.98        36.95 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1626 TCGA-25-1630 TCGA-25-1633 
       33.96         2.99        12.00        15.81         7.86        60.59 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2396 TCGA-25-2398 
       51.22        14.96        24.99        18.05         3.02        45.01 
TCGA-25-2400 TCGA-25-2404 TCGA-29-1691 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       42.02        29.03        47.18         0.79        31.20        68.32 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 
       16.90        18.67        34.62        85.68        62.93        39.12 
TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2425 TCGA-29-2428 
       12.36        14.93         7.23         5.36        65.00        45.11 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1859 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 
       51.91         2.47        48.10        34.78        36.62         1.22 
TCGA-30-1887 TCGA-30-1891 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1575 
       24.26        30.05         6.71        42.51         2.20         8.55 
TCGA-36-1576 TCGA-36-1581 TCGA-36-2537 TCGA-36-2538 TCGA-36-2547 TCGA-36-2552 
       30.08        24.69        25.91        25.08        20.52        11.47 
TCGA-3P-A9WA TCGA-57-1582 TCGA-57-1583 TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 
        7.99        24.03        11.38        29.00        25.02       180.20 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1724 
      116.12         9.40         5.42        20.52         8.09        20.94 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       27.88         4.34        28.47        43.69         1.45         8.42 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1917 TCGA-61-1919 TCGA-61-1998 TCGA-61-2003 
       34.13        31.30        43.43        38.17         5.52         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2102 
       30.64        30.64         4.77        71.74        60.62         6.48 
TCGA-61-2104 TCGA-OY-A56Q TCGA-WR-A838 
       76.87        18.94         8.05 

$`5Q LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
        1.81         2.01        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       48.76        21.57        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       56.55        41.59        38.37       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       55.43        48.89        36.23        31.86        47.70        45.37 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       17.98        35.57         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
       41.62        57.60        61.87        55.36        17.98         5.85 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 
        3.02        97.55        35.15         4.54        71.11        63.09 
TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 
       39.75        26.93        12.46        54.31        25.91        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       33.24        32.28        11.70         3.91        35.44        35.80 
TCGA-10-0937 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 
       15.12        44.55        12.39        31.10        15.19        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0768 TCGA-13-0792 TCGA-13-0795 
        2.50        11.18        11.38         8.45        36.72        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 
        8.71         7.79        35.28        13.61        68.94        74.27 
TCGA-13-0889 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0908 
       61.84        57.47        57.07        47.38        47.84        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0921 TCGA-13-0923 
       37.08        27.72        34.06        29.98         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.08        10.88         6.61         5.92         6.84         4.70 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 
       54.64        87.06        61.71        29.42        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 
       70.82        82.88        73.55        38.20        49.25        37.61 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       13.97        32.84        16.57         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
        2.56         3.91         3.09        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 TCGA-20-1683 TCGA-20-1685 
       54.77         8.42        23.05        72.20        25.38        16.70 
TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1029 TCGA-23-1111 
        2.66        40.54        15.39        31.76         8.81         3.22 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-1809 TCGA-23-2078 
        4.57        33.30         4.27         6.38         0.53        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 
       91.66        77.00        49.84         2.76         4.50         7.63 
TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       19.66        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       63.55        47.41         6.31         6.38         7.82         7.99 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        0.76         6.25         5.95         5.36         4.83        17.39 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1470 TCGA-24-1471 
       18.67        43.53         8.55        72.92         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 
       22.22        26.96        57.40        64.27        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 
       41.39        58.09        88.50        70.62        39.88        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1844 
       45.50        47.70        10.26        90.15        88.37         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.81         4.37        11.28         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 
       22.68        16.44        81.11        44.84        58.16       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-24-2267 
       14.43        18.48        64.01        44.52         0.36        47.54 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 
        0.82        67.36        36.23        55.86        53.26        32.02 
TCGA-25-1316 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 
       37.02        65.00         2.96        18.58        18.02         0.36 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1878 TCGA-25-2042 
       20.61         0.30        56.94        35.54        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 
       49.05         1.02        38.04        12.00        19.99         2.96 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 
       31.00        26.99        78.90        44.71       101.79        38.53 
TCGA-29-1696 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       33.70         0.53        59.67        18.25        41.98        29.23 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       17.00        66.81        31.23        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 
       17.33        11.84        12.30         8.38        34.62        86.17 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       62.47         4.90        42.25        11.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 
       21.04        38.07        36.26        15.68         0.26        44.91 
TCGA-30-1862 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
        6.12        57.57        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       22.49        44.12        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 
       22.55        25.74        27.85        24.23        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       29.49        29.82        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 
       18.31        14.17         6.05        16.18        26.04        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 
        9.44        42.02         7.46        40.77         1.48        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 
        1.74        22.32        25.08        80.12        22.32        34.39 
TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1725 TCGA-61-1727 TCGA-61-1733 
        2.14        44.81        11.11        31.43        18.54        31.79 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1900 
       48.79        44.84        35.80         2.43        33.67         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       11.41        13.02         9.07        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 
       56.61        67.76        15.75         2.01        14.50        17.98 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
       39.85         1.18        45.96        45.40         4.80        51.72 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2109 TCGA-61-2110 
       61.64        58.39        65.52        55.50        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
      125.75        22.22         6.35        31.07         8.61        39.68 
TCGA-VG-A8LO 
        0.79 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.79              0.26 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           180.20            125.75 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            28.47             26.99 
[1] "0.8 - 180.2 (28.5)" "0.3 - 125.8 (27.0)"
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  5Q LOSS MUTATED         1   214                1
  5Q LOSS WILD-TYPE       1   343                1
D50V3, multiclass
                  clus
vv                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  OMENTUM                        1                 1
  OVARY                        214               343
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, continuous
D50V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     1 220
  5Q LOSS WILD-TYPE   2 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1  220
  5Q LOSS WILD-TYPE    2  348
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                1                 2
  YES             220               348
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED    3  4  0  2
  5Q LOSS WILD-TYPE 11 22  5  1
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0               3                11
  R1               4                22
  R2               0                 5
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1     8
  5Q LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED                          11
  5Q LOSS WILD-TYPE                        21
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           0   184
  5Q LOSS WILD-TYPE                                         1   291
D50V7, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   8                10
  BLACK OR AFRICAN AMERICAN                              11                21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 184               291
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5 128
  5Q LOSS WILD-TYPE   5 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5  128
  5Q LOSS WILD-TYPE    5  197
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 5
  NOT HISPANIC OR LATINO             128               197
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    78  80
  6P LOSS WILD-TYPE 188 210
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              158               398 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               80               210 
$`6P LOSS MUTATED`
TCGA-04-1331 TCGA-04-1348 TCGA-04-1351 TCGA-04-1367 TCGA-04-1646 TCGA-04-1649 
       40.24        48.76        65.46        71.47        27.88        64.64 
TCGA-04-1651 TCGA-04-1655 TCGA-09-0365 TCGA-09-1659 TCGA-09-1670 TCGA-09-1672 
       36.23        45.37         9.47         9.99        17.98         5.85 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2053 TCGA-09-2056 TCGA-10-0925 
       97.55         6.18         6.12        39.75        12.46        54.31 
TCGA-10-0926 TCGA-13-0720 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 
       25.91        44.55        17.82        55.17        11.18        11.38 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0801 TCGA-13-0803 TCGA-13-0883 TCGA-13-0884 
       32.25        21.40         8.28        43.86        68.94       107.18 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 
       66.67        70.39        67.99        69.01        57.47        56.15 
TCGA-13-0900 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 
       57.07        47.84        37.08        27.72        14.89         4.64 
TCGA-13-1405 TCGA-13-1410 TCGA-13-1483 TCGA-13-1484 TCGA-13-1491 TCGA-13-1495 
        7.36         4.70        29.42        98.04        52.44        49.25 
TCGA-13-1497 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1512 TCGA-13-2059 
       54.31        32.84         4.21         4.41         3.09        12.23 
TCGA-13-A5FU TCGA-20-1683 TCGA-23-1021 TCGA-23-1030 TCGA-23-1113 TCGA-23-1117 
        8.42        25.38        47.54        29.13        31.20        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2078 
       86.01       129.96        39.09        33.47        24.95        87.48 
TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-1416 TCGA-24-1426 
        2.76         4.70         7.63        11.64         6.38         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1467 
        4.83        17.39        18.67        43.53         8.55       105.99 
TCGA-24-1471 TCGA-24-1546 TCGA-24-1552 TCGA-24-1553 TCGA-24-1560 TCGA-24-1842 
        1.18        64.27        41.39        58.09        44.09         8.32 
TCGA-24-1845 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 
        3.81         5.79        22.68        16.44        11.05         4.87 
TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2271 TCGA-24-2280 TCGA-24-2293 
       44.84       109.71        14.43        31.63        70.45        16.64 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1320 
       55.86        53.26        26.96        51.06        37.02        36.95 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 TCGA-25-1635 TCGA-25-2396 
        2.99         2.96         0.36        20.61        51.22         3.02 
TCGA-25-2399 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 
       19.99        78.90       101.79        38.53        33.70        31.20 
TCGA-29-1707 TCGA-29-1763 TCGA-29-1769 TCGA-29-1775 TCGA-29-1781 TCGA-29-1784 
       41.98        66.81        22.98        12.36         8.38         5.36 
TCGA-29-2428 TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 TCGA-30-1866 
       45.11        38.07        36.26         2.47         0.26        36.62 
TCGA-30-1880 TCGA-31-1951 TCGA-36-1569 TCGA-36-2543 TCGA-36-2548 TCGA-42-2588 
       57.57        22.49        29.10         2.24        14.17         9.44 
TCGA-42-2591 TCGA-59-2350 TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD 
       40.77        22.32       116.12         2.14        44.81        20.52 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       20.94        18.54        27.88        31.79        28.47        48.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 
       35.80         2.43         1.45         8.42         9.07        34.13 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1995 TCGA-61-2008 TCGA-61-2096 
       37.05        48.92        56.61         2.01        30.64        58.39 
TCGA-61-2110 TCGA-61-2613 
       44.52        31.07 

$`6P LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       41.00         1.81        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       11.87        65.52        63.09        21.57        63.98        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 
       32.52        44.32        33.67        76.57        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       41.59        19.99        38.37       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 
       55.43        48.89        28.64        31.86        47.70        29.16 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       57.76        17.98        35.57        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 
       41.62        57.60        61.87        55.36        30.51         3.02 
TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        8.55        35.15         4.54       112.41        71.11        63.09 
TCGA-09-2054 TCGA-09-2055 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       20.94        26.93        81.47        18.51        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       11.70         3.91        35.44        35.80        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
        6.21        24.59        39.58         2.73        12.39        31.10 
TCGA-13-0727 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 
       15.19         2.50        11.54        34.06        31.04         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       38.93        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        7.79         8.12         8.19        35.28        35.28        13.61 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0889 TCGA-13-0893 TCGA-13-0901 TCGA-13-0903 
       91.40        74.27        61.84        43.36        19.36        47.38 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       48.33        44.94        44.84        34.06        29.98        21.17 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 
       13.81         6.41         6.08        10.88         6.61         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        5.92         6.84         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 
       61.71        20.68        22.39        70.82        82.88        73.55 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 
       38.20         4.24        37.61        38.40        13.97        16.57 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 
        4.77         4.18         2.56         3.91        14.24         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 
       10.78         8.75         6.28        54.77        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       26.20        72.20        27.52        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.66        42.54        40.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       49.41         8.81        18.90         2.24        51.35        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 
        3.22        68.68         4.57         4.27         6.38        58.13 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2645 
        0.53       115.89        91.66        77.00        49.84         4.50 
TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 
       19.66        21.80        41.56         7.66        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       63.55        47.41         6.31         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1430 TCGA-24-1431 
        0.76         6.25         6.02         5.95        28.37        19.17 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 
       72.92        12.46        45.14         9.11         3.45        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       26.96        57.40        16.21        56.58        41.06        51.91 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1562 TCGA-24-1563 
       88.50        70.62        39.88        19.53        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 
       38.24         3.48         3.72         4.37        11.28         5.52 
TCGA-24-1920 TCGA-24-1924 TCGA-24-1930 TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 
        9.80        30.21        81.11       152.02        58.16        34.82 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       53.95        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 
       36.16         0.79         0.36        47.54        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1317 
       67.36        36.23        33.11         1.02        32.02         1.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 
       34.98        65.00        33.96        12.00        18.58        18.02 
TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       15.81         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       14.96        24.99        18.05        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 
        1.02        38.04        12.00        45.01        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 
       29.03        31.00        26.99        44.71        47.18         0.79 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32         0.53        16.90        18.67        59.67        18.25 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 
       29.23        34.62        17.00        85.68        62.93        39.12 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 
       31.23        24.36        22.55        17.33        11.84        12.30 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
       14.93         7.23        34.62        86.17        65.00        62.47 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
        4.90        42.25        11.84        11.47         9.76        21.04 
TCGA-30-1718 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       51.91        15.68        48.10        44.91        34.78         6.12 
TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
        1.22        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       18.77         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       21.53        22.85        22.55         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       27.85        24.23        24.69        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 
       29.82        25.91        25.08        23.80        21.60        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       18.31        20.52         6.05        16.18        11.47         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 
       26.04        23.74        42.02         7.46         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       11.38        21.14         1.74        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 
       25.02       180.20        80.12         9.40        34.39         5.42 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 TCGA-61-1737 TCGA-61-1741 
       11.11         8.09        31.43         4.34        44.84        33.67 
TCGA-61-1743 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1911 
       43.69         5.79        11.41        13.02        31.30        42.51 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 
       67.76        43.43        15.75        38.17         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       17.98         4.01        39.85        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
      125.75        22.22         6.35         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.26              0.30 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           129.96            180.20 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           30.855            26.880 
[1] "0.3 - 130.0 (30.9)" "0.3 - 180.2 (26.9)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6P LOSS MUTATED         1   159                0
  6P LOSS WILD-TYPE       1   398                2
D51V3, multiclass
                  clus
vv                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  OMENTUM                        1                 1
  OVARY                        159               398
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, continuous
D51V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1 162
  6P LOSS WILD-TYPE   2 406
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1  162
  6P LOSS WILD-TYPE    2  406
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                1                 2
  YES             162               406
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  6P LOSS MUTATED    1  5  2  0
  6P LOSS WILD-TYPE 13 21  3  3
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0               1                13
  R1               5                21
  R2               2                 3
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     4
  6P LOSS WILD-TYPE                                3    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P LOSS MUTATED                           6
  6P LOSS WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           0   142
  6P LOSS WILD-TYPE                                         1   333
D51V7, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   4                14
  BLACK OR AFRICAN AMERICAN                               6                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 142               333
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2  96
  6P LOSS WILD-TYPE   8 229
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   96
  6P LOSS WILD-TYPE    8  229
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              96               229
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   106 126
  6Q LOSS WILD-TYPE 160 164
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              232               324 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              126               164 
$`6Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1337 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       40.24         2.01        48.76        21.57        63.98        65.46 
TCGA-04-1367 TCGA-04-1517 TCGA-04-1525 TCGA-04-1646 TCGA-04-1649 TCGA-04-1651 
       71.47        19.99        38.37        27.88        64.64        36.23 
TCGA-04-1655 TCGA-09-0365 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       45.37         9.47        17.98         9.99        38.43        89.33 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
       17.98         5.85        97.55         6.18         6.12        35.15 
TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       39.75        26.93        12.46        54.31        25.91        81.47 
TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 
       35.44        19.86        24.59        31.10        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0762 TCGA-13-0766 TCGA-13-0793 TCGA-13-0799 
       11.18        11.38        32.25        21.40        28.70         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 
        8.28         8.19        43.86        68.94       107.18        66.67 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       70.39        67.99        69.01        57.47        56.15        57.07 
TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 TCGA-13-1404 
       47.84        37.08        27.72        14.89         4.64         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 
        7.36         6.05         4.70         4.21        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1491 TCGA-13-1495 TCGA-13-1497 TCGA-13-1501 
       29.42        98.04        52.44        49.25        54.31        32.84 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1512 TCGA-13-2059 TCGA-13-A5FU TCGA-20-1683 
        4.21         4.41         3.09        12.23         8.42        25.38 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 
        2.93        47.54        31.76         8.81        29.13        51.35 
TCGA-23-1113 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 
       31.20        33.30        86.01       129.96        39.09        33.47 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 
       24.95        87.48        49.84         2.76         4.70         7.63 
TCGA-24-0970 TCGA-24-0980 TCGA-24-0982 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 
       11.64         7.66        22.32        47.41         6.38         7.82 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        5.36         4.83        17.39        18.67        43.53         8.55 
TCGA-24-1467 TCGA-24-1471 TCGA-24-1546 TCGA-24-1552 TCGA-24-1553 TCGA-24-1560 
      105.99         1.18        64.27        41.39        58.09        44.09 
TCGA-24-1562 TCGA-24-1564 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1849 
       45.50        25.87         8.32         3.72         3.81         5.79 
TCGA-24-1923 TCGA-24-1927 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2029 
       22.68        16.44         4.87       152.02        44.84        14.43 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 TCGA-24-2293 
        0.79         0.36        31.63        70.45        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       33.11        55.86        53.26        26.96        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
        1.02        34.98        36.95        33.96         2.99        12.00 
TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 TCGA-25-1634 TCGA-25-1878 TCGA-25-2042 
        2.96         0.36        20.61        35.54        85.05        13.02 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2409 TCGA-29-1688 
        3.02        12.00        45.01        19.99        26.99        78.90 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1707 TCGA-29-1762 
      101.79        38.53        33.70        31.20        41.98        85.68 
TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 TCGA-29-1781 
       66.81        31.23        22.98        22.55        12.36         8.38 
TCGA-29-1784 TCGA-29-2428 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
        5.36        45.11        11.84        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1866 TCGA-30-1880 TCGA-31-1951 TCGA-31-1953 
        2.47         0.26        36.62        57.57        22.49         6.71 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1571 TCGA-36-1574 TCGA-36-1580 
       44.12         2.20        29.10        22.85        22.55        24.23 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-42-2588 
       21.60         2.24        18.31        20.52        14.17         9.44 
TCGA-42-2589 TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-59-2350 TCGA-59-2351 
       42.02        40.77        11.38        21.14        22.32       116.12 
TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 
        2.14        44.81        20.52        20.94        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
        4.34        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        2.43         1.45         8.42        13.02         9.07        34.13 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       37.05        48.92        56.61        15.75         2.01         5.52 
TCGA-61-2002 TCGA-61-2008 TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 TCGA-61-2104 
       17.98        30.64        58.39        60.62        55.50        76.87 
TCGA-61-2110 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       44.52        31.07         8.61        39.68 

$`6Q LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       41.00         1.81        49.15        46.62        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       65.52        63.09        49.28        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1530 TCGA-04-1536 
       76.57        82.39        56.55        41.59       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1652 TCGA-04-1654 
       84.20        55.43        48.89        28.64        31.86        47.70 
TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       29.16        57.76        35.57        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1674 TCGA-09-2048 
       61.87        55.36        30.51         3.02         8.55         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-10-0928 TCGA-10-0930 
      112.41        71.11        63.09        20.94        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 
       32.28        11.70         3.91        35.80        15.12         6.21 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        12.39        15.19        17.82 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       11.54        34.06        31.04         8.45        38.93        36.72 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 TCGA-13-0804 TCGA-13-0805 
       30.35        19.59         8.71         8.12        35.28        35.28 
TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 TCGA-13-0889 TCGA-13-0893 TCGA-13-0901 
       13.61        91.40        74.27        61.84        43.36        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 
       47.38        48.33        44.94        44.84        34.06        29.98 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1408 
       21.17        13.81         6.41         6.08        10.88         5.92 
TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
        6.84         5.33        54.64        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 
       82.88        73.55        38.20         4.24        37.61        38.40 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       13.97        16.57         4.77         4.18         2.56         3.91 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       14.24         8.61        10.78         8.75         6.28        54.77 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 
       23.05        25.94        26.20        72.20        27.52        19.10 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       16.70         2.66        42.54        40.54        15.39        26.83 
TCGA-23-1028 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
       49.41        18.90         2.24        54.51         3.22        68.68 
TCGA-23-1116 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
        4.57         4.27         6.38        58.13         0.53       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 
       91.66        77.00         4.50        19.66        21.80        41.56 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
       54.12        63.55         6.31         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1430 TCGA-24-1431 TCGA-24-1463 
        6.25         6.02         5.95        28.37        19.17        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 
       12.46        45.14         9.11         3.45        22.22        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 
       57.40        16.21        56.58        41.06        51.91        88.50 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 
       70.62        39.88        19.53        47.70        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1846 
       90.15        88.37        48.33        38.24         3.48         4.37 
TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 
       11.28         5.52         9.80        30.21        11.05        81.11 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       58.16        34.82       109.71        53.95        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2267 TCGA-24-2281 
       64.01        44.52        57.07        36.16        47.54        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-25-1312 TCGA-25-1314 TCGA-25-1319 TCGA-25-1623 
        0.82        67.36         1.02        32.02        65.00        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       18.02        15.81         7.86         0.30        56.94        60.59 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2391 TCGA-25-2392 
       51.22        14.96        24.99        18.05        49.05         1.02 
TCGA-25-2393 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 
       38.04        42.02         2.96        29.03        31.00        44.71 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       47.18         0.79        68.32         0.53        16.90        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1764 
       59.67        18.25        29.23        34.62        17.00        62.93 
TCGA-29-1766 TCGA-29-1770 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       39.12        24.36        17.33        11.84        12.30        14.93 
TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 
        7.23        34.62        86.17        65.00        62.47         4.90 
TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1859 
       42.25        11.47         9.76        21.04        15.68        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 
       44.91        34.78         6.12         1.22        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1955 TCGA-36-1568 
       48.79        45.57        30.18        18.77        42.51        28.77 
TCGA-36-1570 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 
       21.53         8.55        30.08        25.74        27.85        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       35.05        33.01        29.49        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2544 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       23.80        20.98         6.05        16.18        11.47         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 
       26.04        23.74         7.46         1.48        24.03         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 
        9.40        34.39         5.42        11.11         8.09        31.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1900 TCGA-61-1901 TCGA-61-1907 TCGA-61-1911 
       33.67        43.69         5.79        11.41        31.30        42.51 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 
       67.76        43.43        38.17        14.50         4.01        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2098 TCGA-61-2102 TCGA-61-2109 
       51.72        71.74        61.64        65.52         6.48        20.68 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
      125.75        22.22         6.35        18.94         0.79         8.05 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.26              0.30 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           152.02            180.20 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           27.880            28.275 
[1] "0.3 - 152.0 (27.9)" "0.3 - 180.2 (28.3)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  6Q LOSS MUTATED         2   232                0
  6Q LOSS WILD-TYPE       0   325                2
D52V3, multiclass
                  clus
vv                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  OMENTUM                        2                 0
  OVARY                        232               325
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, continuous
D52V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1 237
  6Q LOSS WILD-TYPE   2 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1  237
  6Q LOSS WILD-TYPE    2  331
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                1                 2
  YES             237               331
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  6Q LOSS MUTATED    4  8  3  0
  6Q LOSS WILD-TYPE 10 18  2  3
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0               4                10
  R1               8                18
  R2               3                 2
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  1    10
  6Q LOSS WILD-TYPE                                2     8
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q LOSS MUTATED                           8
  6Q LOSS WILD-TYPE                        24
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           1   202
  6Q LOSS WILD-TYPE                                         0   273
D52V7, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                  10                 8
  BLACK OR AFRICAN AMERICAN                               8                24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 202               273
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3 142
  6Q LOSS WILD-TYPE   7 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3  142
  6Q LOSS WILD-TYPE    7  183
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 7
  NOT HISPANIC OR LATINO             142               183
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    55  62
  7P LOSS WILD-TYPE 211 228
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              117               439 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               62               228 
$`7P LOSS MUTATED`
TCGA-04-1338 TCGA-04-1347 TCGA-04-1349 TCGA-04-1362 TCGA-04-1638 TCGA-09-0369 
       46.62        63.09        21.57        44.32        55.43        35.57 
TCGA-09-1659 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-10-0928 TCGA-10-0930 
        9.99        57.60        55.36        30.51        18.51        33.24 
TCGA-10-0931 TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 TCGA-13-0751 TCGA-13-0792 
       32.28        35.44        19.86         2.73        55.17        36.72 
TCGA-13-0800 TCGA-13-0885 TCGA-13-0887 TCGA-13-0890 TCGA-13-0897 TCGA-13-0919 
        8.12        91.40        66.67        67.99        57.47        14.89 
TCGA-13-1409 TCGA-13-1487 TCGA-13-1497 TCGA-13-1499 TCGA-13-1505 TCGA-13-1510 
        6.84        22.39        54.31        38.40         4.21         2.56 
TCGA-13-2061 TCGA-20-1685 TCGA-23-1029 TCGA-23-1109 TCGA-23-1114 TCGA-23-1118 
       10.78        16.70         8.81        51.35        68.68        86.01 
TCGA-23-1119 TCGA-23-1122 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-24-0982 
      129.96        39.09        87.48        49.84         2.76        22.32 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1417 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
       63.55        47.41         7.82         5.95         5.36         4.83 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 
       18.67        43.53         8.55        72.92        12.46         9.11 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1562 TCGA-24-1567 TCGA-24-1842 TCGA-24-1843 
       64.27        16.21        45.50        17.23         8.32         3.48 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1930 TCGA-24-2254 TCGA-24-2260 
        3.72         4.37        11.28        81.11        57.07        36.16 
TCGA-24-2262 TCGA-24-2298 TCGA-25-1317 TCGA-25-1321 TCGA-25-1630 TCGA-25-1632 
        0.36        53.26         1.02        33.96         7.86        56.94 
TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 
       60.59        51.22        13.02        49.05         1.02         3.02 
TCGA-25-2399 TCGA-29-1691 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1711 
       19.99        47.18        16.90        18.67        59.67        34.62 
TCGA-29-1761 TCGA-29-1766 TCGA-29-1776 TCGA-29-1781 TCGA-29-2414 TCGA-29-2425 
       17.00        39.12        11.84         8.38        86.17        65.00 
TCGA-29-2431 TCGA-30-1718 TCGA-30-1855 TCGA-30-1887 TCGA-36-1569 TCGA-36-1570 
       42.25        51.91         2.47        24.26        29.10        21.53 
TCGA-36-1574 TCGA-36-1578 TCGA-36-2552 TCGA-42-2589 TCGA-57-1992 TCGA-57-1994 
       22.55        27.85        11.47        42.02        29.00        25.02 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1722 TCGA-61-1724 TCGA-61-1740 
        9.40        34.39         5.42         8.09        20.94         2.43 
TCGA-61-1906 TCGA-61-1913 TCGA-61-1995 TCGA-61-2008 TCGA-61-2009 TCGA-61-2096 
       34.13        48.92         2.01        30.64        39.85        58.39 
TCGA-61-2612 TCGA-OY-A56P TCGA-WR-A838 
        6.35        39.68         8.05 

$`7P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 
       40.24        41.00         1.81        49.15         2.01        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       11.87        65.52        48.76        63.98        65.46        49.28 
TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       32.52        33.67        76.57        71.47        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       41.59        19.99        38.37       119.08        29.10        84.20 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       47.70        45.37        29.16         9.47        57.76        17.98 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1667 TCGA-09-1670 
       38.43        89.33        74.93        41.62        61.87        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       35.15         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        54.31        25.91        81.47 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 
       11.70         3.91        35.80        15.12         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58        12.39        31.10        15.19        17.82 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
        2.50        11.18        11.38        11.54        34.06        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 
       31.04        21.40         8.45        38.93        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       19.59         8.71         7.79         8.28         8.19        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 
       35.28        35.28        13.61        68.94       107.18        74.27 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 
       70.39        61.84        69.01        43.36        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36        47.38        48.33        47.84        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 
       37.08        27.72        34.06        29.98        21.17        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        6.05         5.92         4.70         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 
       87.06        61.71        29.42        98.04        20.68        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
       37.61        13.97        32.84        16.57         4.41         4.77 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         3.91         3.09        14.24        12.23         8.61 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.75         6.28        54.77         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 
       26.20        72.20        27.52        25.38        19.10         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.66        47.54        42.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 
       31.76        49.41        29.13        18.90         2.24        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 
        3.22        31.20         4.57        33.30         4.27         6.38 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 
       33.47        58.13         0.53        24.95       115.89        91.66 
TCGA-23-2081 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
       77.00         4.70         4.50         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 
       21.80        41.56         7.66        54.12         6.31         6.38 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1428 
        7.99         7.86         0.76         6.25         6.02        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 
       28.37        19.17        45.14       105.99         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       22.22        26.96        57.40        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 
       44.09        47.70        25.87        10.26        90.15        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1845 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
       48.33        38.24         3.81         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 
       22.68        30.21        16.44        11.05         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2261 TCGA-24-2267 
       18.48        28.18        64.01        44.52         0.79        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       31.63        70.45        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       16.64        33.11        55.86         1.02        26.96        32.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 
       51.06        37.02        34.98        65.00        36.95         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       12.00         2.96        18.58        18.02        15.81         0.36 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       20.61         0.30        35.54        14.96        24.99        18.05 
TCGA-25-1878 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 
       85.05        38.04        12.00        45.01        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
       29.03        31.00        26.99        78.90        44.71       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       38.53         0.79        33.70        31.20        68.32         0.53 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       18.25        41.98        29.23        85.68        66.81        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       31.23        22.98        24.36        22.55        17.33        12.36 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 
       12.30        14.93         7.23         5.36        34.62        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11         4.90        11.84        11.47         9.76        21.04 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       38.07        36.26        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 
       34.78         6.12        36.62         1.22        57.57        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1571 TCGA-36-1575 
       42.51        44.12         2.20        28.77        22.85         8.55 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       30.08        25.74        24.23        24.69        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       29.49        29.82        25.91        25.08        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
        2.24        20.98        18.31        20.52        14.17         6.05 
TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
       16.18         7.99        26.04        23.74         9.44         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       40.77         1.48        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       22.32        25.08       180.20        80.12        22.32       116.12 
TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1725 TCGA-61-1727 
        2.14        44.81        20.52        11.11        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       35.80        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       11.41        13.02         9.07        31.30        37.05        42.51 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 
       56.61        67.76        43.43        15.75        38.17         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       14.50        17.98         4.01        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.40         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56Q 
       44.52       125.75        22.22        31.07         8.61        18.94 
TCGA-VG-A8LO 
        0.79 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.36              0.26 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           129.96            180.20 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            29.00             27.88 
[1] "0.4 - 130.0 (29.0)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1"  
D53V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7P LOSS MUTATED         0   117                1
  7P LOSS WILD-TYPE       2   440                1
D53V3, multiclass
                  clus
vv                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  OMENTUM                        0                 2
  OVARY                        117               440
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, continuous
D53V5, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0 120
  7P LOSS WILD-TYPE   3 448
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0  120
  7P LOSS WILD-TYPE    3  448
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                0                 3
  YES             120               448
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  7P LOSS MUTATED    4  3  1  0
  7P LOSS WILD-TYPE 10 23  4  3
D53V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0               4                10
  R1               3                23
  R2               1                 4
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  1     5
  7P LOSS WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED                           6
  7P LOSS WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           0   101
  7P LOSS WILD-TYPE                                         1   374
D53V7, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   5                13
  BLACK OR AFRICAN AMERICAN                               6                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                 101               374
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  63
  7P LOSS WILD-TYPE   9 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   63
  7P LOSS WILD-TYPE    9  262
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 9
  NOT HISPANIC OR LATINO              63               262
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    38  43
  7Q LOSS WILD-TYPE 228 247
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               81               475 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               43               247 
$`7Q LOSS MUTATED`
TCGA-04-1349 TCGA-04-1638 TCGA-09-0369 TCGA-09-1659 TCGA-09-1668 TCGA-10-0930 
       21.57        55.43        35.57         9.99        55.36        33.24 
TCGA-10-0931 TCGA-13-0751 TCGA-13-0792 TCGA-13-0800 TCGA-13-0887 TCGA-13-0890 
       32.28        55.17        36.72         8.12        66.67        67.99 
TCGA-13-0897 TCGA-13-0919 TCGA-13-1487 TCGA-13-1499 TCGA-13-1505 TCGA-13-1510 
       57.47        14.89        22.39        38.40         4.21         2.56 
TCGA-13-2061 TCGA-20-1683 TCGA-20-1685 TCGA-23-1029 TCGA-23-1114 TCGA-23-2078 
       10.78        25.38        16.70         8.81        68.68        87.48 
TCGA-23-2084 TCGA-24-0982 TCGA-24-1417 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
       49.84        22.32         7.82         5.95         5.36         4.83 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1469 TCGA-24-1564 TCGA-24-1567 
       18.67        43.53        72.92         9.11        25.87        17.23 
TCGA-24-1842 TCGA-24-1846 TCGA-24-1847 TCGA-24-1930 TCGA-24-2260 TCGA-24-2298 
        8.32         4.37        11.28        81.11        36.16        53.26 
TCGA-25-1317 TCGA-25-1321 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1877 
        1.02        33.96         7.86        56.94        60.59        18.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-29-1691 TCGA-29-1701 
       13.02        49.05         1.02         3.02        47.18        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1776 
       18.67        59.67        17.00        66.81        39.12        11.84 
TCGA-29-1781 TCGA-29-2425 TCGA-29-2431 TCGA-30-1718 TCGA-30-1855 TCGA-30-1887 
        8.38        65.00        42.25        51.91         2.47        24.26 
TCGA-31-1959 TCGA-36-1569 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2552 
        2.20        29.10        25.74        27.85        24.69        11.47 
TCGA-57-1994 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1724 TCGA-61-1995 
       25.02         9.40        34.39         5.42        20.94         2.01 
TCGA-61-2008 TCGA-61-2096 TCGA-61-2612 
       30.64        58.39         6.35 

$`7Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 
       18.51        11.87        65.52        63.09        48.76        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       65.46        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       71.47        82.39        56.55        41.59        19.99        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
      119.08        29.10        84.20        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 
       64.64        36.23        31.86        47.70        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
        9.47        57.76        17.98        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       41.62        57.60        61.87        30.51        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
        3.02         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
        4.54       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       11.70         3.91        35.44        35.80        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
        6.21        24.59        44.55        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       31.10        15.19        17.82         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.54        34.06        32.25        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       38.93        28.70        30.35        19.59         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        43.86        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 
       68.94       107.18        91.40        74.27        70.39        61.84 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       69.01        43.36        56.15        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       48.33        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       34.06        29.98        21.17        13.81         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.08        10.88         6.61         7.36         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 
       61.71        29.42        98.04        20.68        70.82        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
       37.61        13.97        32.84        16.57         4.41         4.77 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         3.91         3.09        14.24        12.23         8.61 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.75         6.28        54.77         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 
       26.20        72.20        27.52        19.10         2.93         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        42.54        40.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       49.41        29.13        18.90         2.24        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
        3.22        31.20         4.57        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
        4.27         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 
       24.95       115.89        91.66        77.00         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
        7.66        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1428 
        7.99         7.86         0.76         6.25         6.02        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       28.37        19.17         8.55        12.46        45.14       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        3.45         1.18        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       16.21        56.58        41.06        51.91        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       88.50        70.62        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       47.70        10.26        90.15        88.37        48.33        38.24 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 
        3.48         3.72         3.81         5.79         5.52         9.80 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 
       22.68        30.21        16.44        11.05         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       44.84        58.16        34.82       109.71        14.43        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 
       18.48        28.18        64.01        44.52        57.07         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 
       67.36        36.23        16.64        33.11        55.86         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 
       26.96        32.02        51.06        37.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       36.95         2.99        12.00         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1634 TCGA-25-1635 
       15.81         0.36        20.61         0.30        35.54        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 
       14.96        24.99        85.05        38.04        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        44.71       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       31.20        68.32         0.53        18.25        41.98        29.23 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       34.62        85.68        62.93        31.23        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 
       22.55        17.33        12.36        12.30        14.93         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
        5.36        34.62        86.17        62.47        45.11         4.90 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 
       11.84        11.47         9.76        21.04        38.07        36.26 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       15.68         0.26        48.10        44.91        34.78         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
       36.62         1.22        57.57        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       28.77        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.23        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 
       20.52        14.17         6.05        16.18         7.99        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74         9.44        42.02         7.46        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       24.03        11.38        21.14         1.74        22.32        29.00 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2355 
       25.08       180.20        80.12        22.32       116.12         2.14 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 
       44.81        20.52        11.11         8.09        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       27.88         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       35.80         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 
       37.05        42.51        48.92        56.61        67.76        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       15.75        38.17         5.52        14.50        17.98         4.01 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       39.85        30.64         1.18        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 
        4.77        51.72        71.74        61.64        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       55.50         6.48        76.87        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       22.22        31.07         8.61        39.68        18.94         0.79 
TCGA-WR-A838 
        8.05 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1.02              0.26 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            87.48            180.20 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            24.26             29.00 
[1] "1.0 - 87.5 (24.3)"  "0.3 - 180.2 (29.0)"
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  7Q LOSS MUTATED         0    80                1
  7Q LOSS WILD-TYPE       2   477                1
D54V3, multiclass
                  clus
vv                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         80               477
  PERITONEUM OVARY               1                 1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, continuous
D54V5, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  80
  7Q LOSS WILD-TYPE   2 488
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   80
  7Q LOSS WILD-TYPE    2  488
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1                 2
  YES              80               488
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  7Q LOSS MUTATED    3  2  0  0
  7Q LOSS WILD-TYPE 11 24  5  3
D54V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               3                11
  R1               2                24
  R2               0                 5
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  1     5
  7Q LOSS WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED                           4
  7Q LOSS WILD-TYPE                        28
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           0    68
  7Q LOSS WILD-TYPE                                         1   407
D54V7, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   5                13
  BLACK OR AFRICAN AMERICAN                               4                28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  68               407
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0  44
  7Q LOSS WILD-TYPE  10 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0   44
  7Q LOSS WILD-TYPE   10  281
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                10
  NOT HISPANIC OR LATINO              44               281
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   122 144
  8P LOSS WILD-TYPE 144 146
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              266               290 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              144               146 
$`8P LOSS MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1346 TCGA-04-1348 TCGA-04-1356 TCGA-04-1361 
       41.00        46.62        65.52        48.76        49.28        32.52 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1530 
       76.57        71.47        82.39        56.55        19.99       119.08 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 TCGA-09-0366 
       29.10        55.43        27.88        31.86        45.37        57.76 
TCGA-09-0367 TCGA-09-1661 TCGA-09-1664 TCGA-09-1668 TCGA-09-1670 TCGA-09-1674 
       17.98        38.43        74.93        55.36        17.98         8.55 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2056 TCGA-10-0925 TCGA-10-0927 
       71.11        63.09        20.94        12.46        54.31        81.47 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0936 TCGA-13-0723 TCGA-13-0725 
       18.51        33.24        32.28        35.80        39.58        12.39 
TCGA-13-0730 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0792 
       17.82        11.18        11.54        34.06        32.25        36.72 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 
       28.70        19.59         8.19        43.86        35.28        13.61 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 
       68.94        91.40        66.67        70.39        67.99        56.15 
TCGA-13-0901 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       19.36        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 
        6.08        10.88         6.05         4.70         4.21        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1494 TCGA-13-1495 
       61.71        29.42        98.04        22.39        38.20        49.25 
TCGA-13-1496 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
        4.24        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
        4.77         4.18         2.56        12.23        10.78         8.75 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1684 TCGA-20-1686 
       54.77         8.42        25.94        26.20        19.10         2.93 
TCGA-23-1021 TCGA-23-1024 TCGA-23-1031 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 
       47.54        15.39        18.90        68.68         4.57         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        6.38        39.09        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2643 TCGA-23-2645 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 
      115.89         4.70         4.50        21.80         7.66        22.32 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1422 
       63.55         6.31         6.38         7.82         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
        6.25         6.02         4.83        17.39        19.17        18.67 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1544 TCGA-24-1546 
        8.55        12.46       105.99         3.45        26.96        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1558 TCGA-24-1604 
       16.21        56.58        41.06        41.39        19.53        88.37 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1846 TCGA-24-1850 TCGA-24-1924 
       48.33         8.32         3.72         4.37         5.52        30.21 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 
       16.44        11.05        81.11        58.16       109.71        53.95 
TCGA-24-2035 TCGA-24-2254 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 
       28.18        57.07         0.79        47.54        70.45        44.61 
TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-25-1313 TCGA-25-1314 
        0.82        36.23        16.64        33.11        26.96        32.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1626 
       34.98        65.00        33.96         2.99        12.00        15.81 
TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 
        0.36         7.86         0.30        60.59        51.22        24.99 
TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 
       85.05        38.04         3.02        19.99        42.02        29.03 
TCGA-25-2409 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       26.99        47.18        38.53         0.79        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1761 
        0.53        16.90        59.67        18.25        29.23        17.00 
TCGA-29-1762 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1783 
       85.68        31.23        24.36        17.33        12.36         7.23 
TCGA-29-1784 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-30-1855 
        5.36        45.11         4.90        11.84        11.47         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1862 TCGA-30-1866 TCGA-30-1887 TCGA-31-1944 
       15.68         0.26         6.12        36.62        24.26        45.57 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       18.77        22.49        42.51        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-2534 TCGA-36-2537 
       22.55         8.55        25.74        24.23        29.82        25.91 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2547 TCGA-36-2552 TCGA-3P-A9WA 
       25.08        21.60         2.24        20.52        11.47         7.99 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 
       23.74         9.44        42.02         7.46         1.48        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.74        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-A5PD TCGA-61-1727 TCGA-61-1728 
       22.32       116.12         9.40        20.52        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 
        4.34        31.79        44.84         2.43        33.67         1.45 
TCGA-61-1904 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 
        9.07        56.61        67.76        38.17         5.52        14.50 
TCGA-61-2008 TCGA-61-2016 TCGA-61-2018 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       30.64         1.18        45.40        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 
        6.48        76.87        20.68        44.52        22.22        31.07 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

$`8P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       40.24         1.81        49.15         2.01        18.51        11.87 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1362 TCGA-04-1364 
       63.09        21.57        63.98        65.46        44.32        33.67 
TCGA-04-1516 TCGA-04-1525 TCGA-04-1542 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 
       41.59        38.37        84.20        48.89        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-09-1659 
       36.23        47.70        29.16         9.47        35.57         9.99 
TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1672 
       89.33        41.62        57.60        61.87        30.51         5.85 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        3.02        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2053 TCGA-09-2055 TCGA-10-0926 TCGA-10-0933 TCGA-10-0934 
      112.41        39.75        26.93        25.91        11.70         3.91 
TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        15.12        19.86         6.21        24.59        44.55 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 
        2.73        31.10        15.19        55.17         2.50        11.38 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0794 TCGA-13-0797 
       31.04        21.40         8.45        38.93        30.35         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0804 TCGA-13-0884 TCGA-13-0886 
        7.79         8.12         8.28        35.28       107.18        74.27 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 
       61.84        69.01        43.36        57.47        57.07        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       48.33        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0921 TCGA-13-0923 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 
        4.64         6.41         6.61         7.36         5.92         6.84 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
        5.33        54.64        20.68        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1497 TCGA-13-1498 TCGA-13-1506 TCGA-13-1511 TCGA-13-1512 
       73.55        54.31        37.61         4.41         3.91         3.09 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2071 TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 
       14.24         8.61         6.28        23.05        72.20        27.52 
TCGA-20-1683 TCGA-20-1685 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 
       25.38        16.70         2.66        42.54        40.54        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 
       31.76        49.41         8.81        29.13         2.24        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       54.51         3.22        31.20        33.30        86.01       129.96 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 
       87.48        91.66        77.00        49.84         2.76         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0979 TCGA-24-1103 TCGA-24-1105 TCGA-24-1418 
       19.66        11.64        41.56        54.12        47.41         7.99 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 TCGA-24-1466 
        5.95         5.36        28.37        43.53        72.92        45.14 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1551 TCGA-24-1553 
        9.11         1.18        22.22        57.40        51.91        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       88.50        70.62        39.88        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 TCGA-24-1843 
       25.87        10.26        17.23        90.15        38.24         3.48 
TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-2019 
        3.81        11.28         5.79         9.80        22.68         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 TCGA-24-2029 TCGA-24-2033 TCGA-24-2036 
      152.02        44.84        34.82        14.43        18.48        64.01 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 TCGA-24-2289 TCGA-24-2297 
       44.52        36.16         0.36        31.63        67.36        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 
       53.26         1.02        51.06        37.02         1.02        36.95 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1632 TCGA-25-1634 
        2.96        18.58        18.02        20.61        56.94        35.54 
TCGA-25-1870 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 
       14.96        18.05        13.02        49.05         1.02        12.00 
TCGA-25-2398 TCGA-25-2401 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
       45.01         2.96        31.00        78.90        44.71       101.79 
TCGA-29-1696 TCGA-29-1702 TCGA-29-1707 TCGA-29-1711 TCGA-29-1763 TCGA-29-1764 
       33.70        18.67        41.98        34.62        66.81        62.93 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       39.12        22.98        22.55        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 
        8.38        34.62        86.17        65.00        62.47        42.25 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1859 
        9.76        21.04        38.07        51.91        36.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
       44.91        34.78         1.22        57.57        30.05        48.79 
TCGA-31-1946 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1576 
       30.18         6.71        44.12         2.20        28.77        30.08 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2540 
       27.85        24.69        35.05        33.01        29.49        23.80 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 
       20.98        18.31        14.17         6.05        16.18        26.04 
TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-59-2349 TCGA-59-2354 TCGA-59-2355 
       40.77        24.03        21.14        80.12        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        5.42        44.81        11.11         8.09        20.94        31.43 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 
       28.47        48.79        35.80        43.69         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       11.41        13.02        34.13        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-2002 TCGA-61-2003 
       48.92        43.43        15.75         2.01        17.98         4.01 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
       39.85        30.64        45.96         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 
       71.74        61.64        58.39       125.75         6.35         8.61 
TCGA-OY-A56P TCGA-OY-A56Q 
       39.68        18.94 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.26              0.36 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           180.20            152.02 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            24.31             31.07 
[1] "0.3 - 180.2 (24.3)" "0.4 - 152.0 (31.1)"
[1] "hr=" "1.2"
D55V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8P LOSS MUTATED         2   266                0
  8P LOSS WILD-TYPE       0   291                2
D55V3, multiclass
                  clus
vv                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  OMENTUM                        2                 0
  OVARY                        266               291
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, continuous
D55V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1 272
  8P LOSS WILD-TYPE   2 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1  272
  8P LOSS WILD-TYPE    2  296
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                1                 2
  YES             272               296
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED    5 12  4  2
  8P LOSS WILD-TYPE  9 14  1  1
D55V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0               5                 9
  R1              12                14
  R2               4                 1
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  2     8
  8P LOSS WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P LOSS MUTATED                          17
  8P LOSS WILD-TYPE                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           1   224
  8P LOSS WILD-TYPE                                         0   251
D55V7, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 1
  ASIAN                                                   8                10
  BLACK OR AFRICAN AMERICAN                              17                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 224               251
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     6 148
  8P LOSS WILD-TYPE   4 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      6  148
  8P LOSS WILD-TYPE    4  177
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 4
  NOT HISPANIC OR LATINO             148               177
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    38  48
  8Q LOSS WILD-TYPE 228 242
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               86               470 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               48               242 
$`8Q LOSS MUTATED`
TCGA-04-1332 TCGA-04-1346 TCGA-04-1356 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       41.00        65.52        49.28        82.39        56.55        19.99 
TCGA-04-1655 TCGA-09-0366 TCGA-09-2051 TCGA-09-2054 TCGA-10-0928 TCGA-13-0725 
       45.37        57.76        63.09        20.94        18.51        12.39 
TCGA-13-0730 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0803 TCGA-13-0885 
       17.82        11.18        11.54        32.25        43.86        91.40 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0901 TCGA-13-0913 TCGA-13-0920 TCGA-13-1407 
       66.67        70.39        19.36        29.98        13.81         6.05 
TCGA-13-1483 TCGA-13-1510 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-1684 
       29.42         2.56        10.78         8.75        54.77        19.10 
TCGA-23-1032 TCGA-23-1114 TCGA-23-1122 TCGA-23-1809 TCGA-24-0980 TCGA-24-0982 
        2.24        68.68        39.09         0.53         7.66        22.32 
TCGA-24-1416 TCGA-24-1424 TCGA-24-1427 TCGA-24-1431 TCGA-24-1544 TCGA-24-1548 
        6.38         6.02         4.83        19.17        26.96        16.21 
TCGA-24-1842 TCGA-24-1850 TCGA-24-1928 TCGA-24-2030 TCGA-24-2254 TCGA-24-2261 
        8.32         5.52        11.05        53.95        57.07         0.79 
TCGA-24-2267 TCGA-24-2280 TCGA-25-1318 TCGA-25-1319 TCGA-25-1322 TCGA-25-1626 
       47.54        70.45        34.98        65.00         2.99        15.81 
TCGA-25-1630 TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-2393 TCGA-25-2400 
        7.86        35.54        51.22        24.99        38.04        42.02 
TCGA-25-2409 TCGA-29-1691 TCGA-29-1770 TCGA-29-1775 TCGA-29-2428 TCGA-30-1855 
       26.99        47.18        24.36        12.36        45.11         2.47 
TCGA-31-1955 TCGA-36-1571 TCGA-36-1575 TCGA-36-2537 TCGA-36-2547 TCGA-36-2552 
       42.51        22.85         8.55        25.91        20.52        11.47 
TCGA-42-2587 TCGA-42-2589 TCGA-57-1994 TCGA-59-2352 TCGA-61-1727 TCGA-61-1730 
       23.74        42.02        25.02         9.40        18.54         4.34 
TCGA-61-1733 TCGA-61-1904 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2110 
       31.79         9.07        60.62        55.50         6.48        44.52 
TCGA-61-2113 TCGA-WR-A838 
       22.22         8.05 

$`8Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24         1.81        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       11.87        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1516 
       32.52        44.32        33.67        76.57        71.47        41.59 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       38.37       119.08        29.10        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
       29.16         9.47        17.98        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       89.33        74.93        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       30.51        17.98         5.85         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        6.18         6.12        35.15         4.54       112.41        71.11 
TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       39.75        26.93        12.46        54.31        25.91        81.47 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       33.24        32.28        11.70         3.91        35.44        35.80 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       15.12        19.86         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 
        2.73        31.10        15.19        55.17         2.50        11.38 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       34.06        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       28.70        30.35        19.59         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.28         8.19        35.28        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
      107.18        74.27        61.84        67.99        69.01        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       57.47        56.15        57.07        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 
       44.94        44.84        37.08        27.72        34.06        21.17 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        7.36         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       54.64        87.06        61.71        98.04        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
        4.24        54.31        37.61        38.40        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 
       16.57         4.21         4.41         4.77         4.18         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FU 
        3.09        14.24        12.23         8.61         6.28         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       23.05        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       16.70         2.93         2.66        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
       18.90        51.35        54.51         3.22        31.20         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 
       33.30        86.01       129.96         4.27         6.38        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       58.13        24.95       115.89        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 
       49.84         2.76         4.70         4.50         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       11.64        21.80        41.56        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.31         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        5.95         5.36        17.39        28.37        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
        8.55        72.92        12.46        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 
        3.45         1.18        22.22        57.40        64.27        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       10.26        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        3.48         3.72         3.81         4.37        11.28         5.79 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 
        9.80        22.68        30.21        16.44        81.11         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
      152.02        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 
       18.48        28.18        64.01        44.52        36.16         0.36 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       31.63        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       33.11        55.86        53.26         1.02        26.96        32.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 
       51.06        37.02         1.02        36.95        33.96        12.00 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
        2.96        18.58        18.02         0.36        20.61         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       56.94        60.59        14.96        18.05        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       49.05         1.02         3.02        12.00        45.01        19.99 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
        2.96        29.03        31.00        78.90        44.71       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       38.53         0.79        33.70        31.20        68.32         0.53 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       16.90        18.67        59.67        18.25        41.98        29.23 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       34.62        17.00        85.68        66.81        62.93        39.12 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 
       31.23        22.98        22.55        17.33        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 
       14.93         8.38         7.23         5.36        34.62        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       65.00        62.47         4.90        42.25        11.84        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 
        9.76        21.04        38.07        51.91        36.26        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 
        0.26        48.10        44.91        34.78         6.12        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 
       30.18        18.77        22.49         6.71        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 
       28.77        29.10        21.53        22.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       27.85        24.23        24.69        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       29.82        25.08        23.80        21.60         2.24        20.98 
TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 
       18.31        14.17         6.05        16.18         7.99        26.04 
TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
        9.44         7.46        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 
       21.14         1.74        22.32        29.00        25.08       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       80.12        22.32       116.12        34.39         2.14         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       44.81        20.52        11.11         8.09        20.94        31.43 
TCGA-61-1728 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       27.88        28.47        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       33.67        43.69         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       13.02        34.13        31.30        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       56.61        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        5.52        14.50        17.98         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2104 
       51.72        71.74        61.64        58.39        65.52        76.87 
TCGA-61-2109 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       20.68       125.75         6.35        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO 
       18.94         0.79 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.53              0.26 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             91.4             180.2 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           23.295            29.015 
[1] "0.5 - 91.4 (23.3)"  "0.3 - 180.2 (29.0)"
[1] "hr=" "1.3"
D56V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  8Q LOSS MUTATED         0    86                0
  8Q LOSS WILD-TYPE       2   471                2
D56V3, multiclass
                  clus
vv                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  OMENTUM                        0                 2
  OVARY                         86               471
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, continuous
D56V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  89
  8Q LOSS WILD-TYPE   3 479
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   89
  8Q LOSS WILD-TYPE    3  479
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 3
  YES              89               479
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  8Q LOSS MUTATED    3  3  0  1
  8Q LOSS WILD-TYPE 11 23  5  2
D56V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               3                11
  R1               3                23
  R2               0                 5
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     1
  8Q LOSS WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q LOSS MUTATED                           6
  8Q LOSS WILD-TYPE                        26
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           0    74
  8Q LOSS WILD-TYPE                                         1   401
D56V7, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 3
  ASIAN                                                   1                17
  BLACK OR AFRICAN AMERICAN                               6                26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 1
  WHITE                                                  74               401
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     2  47
  8Q LOSS WILD-TYPE   8 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2   47
  8Q LOSS WILD-TYPE    8  278
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 8
  NOT HISPANIC OR LATINO              47               278
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   116 136
  9P LOSS WILD-TYPE 150 154
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              252               304 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              136               154 
$`9P LOSS MUTATED`
TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       41.00         2.01        46.62        11.87        65.52        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 
       21.57        63.98        65.46        49.28        32.52        33.67 
TCGA-04-1371 TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       82.39        19.99        38.37        29.10        84.20        55.43 
TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 
       27.88        64.64        31.86        29.16         9.47        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1667 
       35.57         9.99        38.43        89.33        41.62        61.87 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2049 
       30.51        17.98         3.02        97.55         6.12       112.41 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0927 TCGA-10-0930 
       39.75        20.94        26.93        12.46        81.47        33.24 
TCGA-10-0931 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0724 TCGA-13-0760 
       32.28        19.86         6.21        24.59         2.73        11.54 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0805 
       32.25        31.04        19.59         8.12        35.28        35.28 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       68.94        91.40        74.27        70.39        61.84        67.99 
TCGA-13-0900 TCGA-13-0904 TCGA-13-0908 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 
       57.07        48.33        44.84         4.64         6.08        10.88 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 
       87.06        29.42        98.04        20.68        22.39        82.88 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1500 TCGA-13-1509 TCGA-13-2057 
       52.44        38.20        49.25        13.97         4.18        14.24 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-1682 
        8.61        10.78         8.75        54.77         8.42        27.52 
TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1027 TCGA-23-1028 
       19.10        16.70        47.54        42.54        31.76        49.41 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
       29.13        18.90        68.68         4.57        86.01       129.96 
TCGA-23-2072 TCGA-23-2081 TCGA-23-2643 TCGA-23-2645 TCGA-24-0982 TCGA-24-1105 
       24.95        77.00         4.70         4.50        22.32        47.41 
TCGA-24-1413 TCGA-24-1419 TCGA-24-1422 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 
        6.31         7.86         0.76         5.36         4.83        28.37 
TCGA-24-1431 TCGA-24-1463 TCGA-24-1464 TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 
       19.17        72.92        12.46        57.40        64.27        56.58 
TCGA-24-1550 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 TCGA-24-1604 
       41.06        44.09        47.70        25.87        90.15        88.37 
TCGA-24-1843 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 
        3.48        81.11         4.87        44.84        58.16        14.43 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
       53.95        28.18        64.01        36.16         0.79        47.54 
TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 
       16.64        33.11         1.02        32.02        37.02         1.02 
TCGA-25-1318 TCGA-25-1321 TCGA-25-1323 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       34.98        33.96        12.00        18.02        15.81         0.36 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2392 
       60.59        35.54        14.96        24.99        18.05         1.02 
TCGA-25-2393 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-29-1688 TCGA-29-1693 
       38.04        19.99        42.02         2.96        78.90       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1705 
       38.53         0.79        68.32         0.53        18.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       41.98        29.23        39.12        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1783 TCGA-29-2425 TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 
       12.36         7.23        65.00        11.47         9.76        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1861 TCGA-30-1866 
       51.91        36.26        15.68         0.26        34.78        36.62 
TCGA-30-1880 TCGA-30-1891 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 
       57.57        30.05         6.71        42.51         2.20        29.10 
TCGA-36-1571 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 TCGA-36-2537 TCGA-36-2540 
       22.85        30.08        24.23        35.05        25.91        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 
       21.60        20.98        20.52        14.17         6.05        11.47 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 
       42.02         7.46         1.48        24.03        11.38         1.74 
TCGA-57-1992 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 
       29.00        25.02       116.12         9.40         2.14         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
       44.81        20.52        27.88         4.34        31.79        48.79 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1907 TCGA-61-1910 TCGA-61-1914 TCGA-61-1915 
        8.42         5.79        31.30        37.05        56.61        67.76 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       15.75        38.17         2.01        14.50        17.98         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2095 TCGA-61-2096 
       30.64        39.85        30.64         1.18        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2113 TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       22.22         6.35        39.68        18.94         0.79         8.05 

$`9P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1342 TCGA-04-1348 TCGA-04-1362 
       40.24         1.81        49.15        18.51        48.76        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1530 TCGA-04-1644 
       76.57        71.47        56.55        41.59       119.08        48.89 
TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-1664 
       28.64        36.23        47.70        45.37        57.76        74.93 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 
       57.60        55.36         5.85         8.55         6.18        35.15 
TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 
        4.54        71.11        63.09        54.31        25.91        18.51 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0720 
       11.70         3.91        35.44        35.80        15.12        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58        12.39        31.10        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 
        2.50        11.18        11.38        34.06        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       38.93        36.72        28.70        30.35         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0807 TCGA-13-0884 TCGA-13-0887 
        8.28         8.19        43.86        13.61       107.18        66.67 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 
       69.01        43.36        57.47        56.15        19.36        47.38 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       47.84        44.94        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-1404 TCGA-13-1405 
       21.17        14.89        13.81         6.41         6.61         7.36 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1488 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 
       54.64        61.71        70.82        73.55         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2071 
        4.77         2.56         3.91         3.09        12.23         6.28 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1686 
       23.05        25.94        26.20        72.20        25.38         2.93 
TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 TCGA-23-1032 
        2.66        40.54        15.39        26.83         8.81         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1117 TCGA-23-1120 
       51.35        54.51         3.22        31.20        33.30         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
        6.38        39.09        33.47        58.13         0.53       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0968 
       87.48        91.66        49.84         2.76         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
       11.64        21.80        41.56         7.66        54.12        63.55 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        6.38         7.82         7.99         6.25         6.02         5.95 
TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 
       17.39        18.67        43.53         8.55        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 
        9.11         3.45         1.18        22.22        26.96        16.21 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 TCGA-24-1614 TCGA-24-1616 
       19.53        45.50        10.26        17.23        48.33        38.24 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        8.32         3.72         3.81         4.37        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2027 TCGA-24-2033 TCGA-24-2038 TCGA-24-2254 
      152.02        34.82       109.71        18.48        44.52        57.07 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
        0.36        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1319 
       36.23        55.86        53.26        26.96        51.06        65.00 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1628 TCGA-25-1630 
       36.95         2.99         2.96        18.58        20.61         7.86 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1635 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
        0.30        56.94        51.22        85.05        13.02        49.05 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
        3.02        12.00        45.01        29.03        31.00        26.99 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 
       44.71        47.18        33.70        31.20        16.90        59.67 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 
       34.62        17.00        85.68        66.81        62.93        31.23 
TCGA-29-1769 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 
       22.98        11.84        12.30        14.93         8.38         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       34.62        86.17        62.47        45.11         4.90        42.25 
TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 
       11.84        21.04         2.47        48.10        44.91         6.12 
TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
        1.22        24.26        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 
       22.49        44.12        28.77        21.53        22.55         8.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       25.74        27.85        24.69        33.01        29.49        29.82 
TCGA-36-2538 TCGA-36-2543 TCGA-36-2545 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 
       25.08         2.24        18.31        16.18         7.99        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 
       23.74         9.44        40.77        21.14        22.32        25.08 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-61-1721 TCGA-61-1722 
      180.20        80.12        22.32        34.39        11.11         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 
       20.94        31.43        18.54        28.47        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1901 TCGA-61-1903 
        2.43        33.67        43.69         1.45        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 TCGA-61-1913 TCGA-61-1917 TCGA-61-1998 
        9.07        34.13        42.51        48.92        43.43         5.52 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        31.07         8.61 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.26              0.30 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           129.96            180.20 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           28.275            27.785 
[1] "0.3 - 130.0 (28.3)" "0.3 - 180.2 (27.8)"
[1] "hr=" "1"  
D57V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  9P LOSS MUTATED         1   253                2
  9P LOSS WILD-TYPE       1   304                0
D57V3, multiclass
                  clus
vv                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  OMENTUM                        1                 1
  OVARY                        253               304
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, continuous
D57V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2 260
  9P LOSS WILD-TYPE   1 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2  260
  9P LOSS WILD-TYPE    1  308
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                2                 1
  YES             260               308
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED    8  9  4  2
  9P LOSS WILD-TYPE  6 17  1  1
D57V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0               8                 6
  R1               9                17
  R2               4                 1
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  1     7
  9P LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P LOSS MUTATED                          17
  9P LOSS WILD-TYPE                        15
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           1   212
  9P LOSS WILD-TYPE                                         0   263
D57V7, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   7                11
  BLACK OR AFRICAN AMERICAN                              17                15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 212               263
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     6 152
  9P LOSS WILD-TYPE   4 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6  152
  9P LOSS WILD-TYPE    4  173
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 4
  NOT HISPANIC OR LATINO             152               173
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   127 146
  9Q LOSS WILD-TYPE 139 144
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              273               283 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              146               144 
$`9Q LOSS MUTATED`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 
       41.00        49.15         2.01        46.62        11.87        65.52 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       63.09        21.57        63.98        65.46        49.28        32.52 
TCGA-04-1364 TCGA-04-1371 TCGA-04-1517 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 
       33.67        82.39        19.99        38.37        84.20        55.43 
TCGA-04-1646 TCGA-04-1649 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 
       27.88        64.64        45.37        29.16         9.47        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 
       35.57         9.99        38.43        61.87        30.51        17.98 
TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2049 TCGA-09-2053 
        3.02         8.55        97.55         6.12       112.41        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-10-0927 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 
       20.94        26.93        81.47        35.80        19.86         6.21 
TCGA-13-0717 TCGA-13-0724 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 
       24.59         2.73        55.17        11.18        11.54        32.25 
TCGA-13-0764 TCGA-13-0768 TCGA-13-0793 TCGA-13-0795 TCGA-13-0800 TCGA-13-0803 
       31.04         8.45        28.70        19.59         8.12        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       35.28        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0899 TCGA-13-0900 TCGA-13-0904 
       74.27        70.39        61.84        56.15        57.07        48.33 
TCGA-13-0908 TCGA-13-0913 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       44.84        29.98         4.64         6.41         6.08        10.88 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1483 
        6.05         5.92         6.84         4.70         4.21        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1495 TCGA-13-1499 
       98.04        22.39        82.88        52.44        49.25        38.40 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1507 TCGA-13-1509 TCGA-13-2057 TCGA-13-2060 
       13.97        16.57         4.77         4.18        14.24         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-1682 
       10.78         8.75        54.77         8.42        25.94        27.52 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1028 
       19.10        16.70         2.93        47.54        42.54        49.41 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 
       29.13        18.90         3.22        68.68         4.57        86.01 
TCGA-23-1119 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2643 TCGA-23-2645 
      129.96        33.47        24.95       115.89         4.70         4.50 
TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 
       19.66        21.80        41.56        22.32        47.41         6.31 
TCGA-24-1417 TCGA-24-1422 TCGA-24-1424 TCGA-24-1426 TCGA-24-1431 TCGA-24-1464 
        7.82         0.76         6.02         5.36        19.17        12.46 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1549 TCGA-24-1550 
        9.11         1.18        26.96        57.40        56.58        41.06 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 
       19.53        44.09        45.50        47.70        25.87        90.15 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1924 TCGA-24-1928 
       88.37        38.24         3.48         3.81        30.21        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 
       81.11         4.87        44.84        58.16        34.82        14.43 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2288 
       18.48        28.18        36.16         0.79        47.54         0.82 
TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 
       16.64        33.11         1.02        32.02        37.02         1.02 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1626 TCGA-25-1627 
       34.98        36.95        33.96        12.00        15.81         0.36 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
        7.86         0.30        60.59        35.54        14.96        24.99 
TCGA-25-1877 TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       18.05         1.02        38.04        45.01        19.99        42.02 
TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 
       78.90       101.79        38.53         0.79        68.32         0.53 
TCGA-29-1702 TCGA-29-1705 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 
       18.67        18.25        29.23        17.00        66.81        39.12 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 
       24.36        22.55        17.33        12.36        12.30         7.23 
TCGA-29-2425 TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 
       65.00        11.47        38.07        36.26        15.68         0.26 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-31-1944 TCGA-31-1950 
       34.78        36.62         1.22        57.57        45.57        18.77 
TCGA-31-1953 TCGA-31-1955 TCGA-36-1569 TCGA-36-1571 TCGA-36-1576 TCGA-36-1580 
        6.71        42.51        29.10        22.85        30.08        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2537 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       24.69        35.05        25.91         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2589 TCGA-42-2590 
       20.52        14.17         6.05        11.47        42.02         7.46 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 TCGA-57-1992 TCGA-59-2351 TCGA-59-2352 
        1.48        24.03         1.74        29.00       116.12         9.40 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1730 TCGA-61-1733 
        2.14         5.42        44.81        20.52         4.34        31.79 
TCGA-61-1736 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 
       48.79        33.67        43.69         8.42         9.07        34.13 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-2000 
       56.61        67.76        15.75        38.17         2.01        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2094 
       17.98         4.01        39.85        30.64         1.18        71.74 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       58.39        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
       39.68        18.94         8.05 

$`9Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1342 TCGA-04-1348 TCGA-04-1362 TCGA-04-1365 
       40.24         1.81        18.51        48.76        44.32        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1530 TCGA-04-1536 TCGA-04-1644 
       71.47        56.55        41.59       119.08        29.10        48.89 
TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-0366 TCGA-09-1662 
       28.64        36.23        31.86        47.70        57.76        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1672 TCGA-09-2043 
       74.93        41.62        57.60        55.36         5.85         6.18 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2056 TCGA-10-0925 
       35.15         4.54        71.11        63.09        12.46        54.31 
TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       25.91        18.51        33.24        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0937 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 
       35.44        15.12        44.55        39.58        12.39        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0766 
       15.19        17.82         2.50        11.38        34.06        21.40 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       38.93        36.72        30.35         8.71         7.79         8.28 
TCGA-13-0802 TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
        8.19        66.67        67.99        69.01        43.36        57.47 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 
       19.36        47.38        47.84        44.94        37.08        27.72 
TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-1404 TCGA-13-1405 
       34.06        21.17        14.89        13.81         6.61         7.36 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 TCGA-13-1488 
        5.33        54.64        87.06        61.71        20.68        70.82 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1501 
       73.55        38.20         4.24        54.31        37.61        32.84 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
        4.21         4.41         2.56         3.91         3.09        12.23 
TCGA-13-2071 TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1687 
        6.28        23.05        26.20        72.20        25.38         2.66 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 TCGA-23-1032 
       40.54        15.39        26.83        31.76         8.81         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 
       51.35        54.51        31.20        33.30         4.27         6.38 
TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       39.09        58.13         0.53        87.48        91.66        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0980 TCGA-24-1103 
       49.84         2.76         7.63        11.64         7.66        54.12 
TCGA-24-1104 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 
       63.55         6.38         7.99         7.86         6.25         5.95 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        4.83        17.39        28.37        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1546 
       72.92        45.14       105.99         3.45        22.22        64.27 
TCGA-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       16.21        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1565 TCGA-24-1567 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 
       39.88        10.26        17.23        48.33         8.32         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        4.37        11.28         5.79         5.52         9.80        22.68 
TCGA-24-1927 TCGA-24-2020 TCGA-24-2027 TCGA-24-2030 TCGA-24-2036 TCGA-24-2038 
       16.44       152.02       109.71        53.95        64.01        44.52 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 
       57.07         0.36        31.63        70.45        44.61        67.36 
TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1319 
       36.23        55.86        53.26        26.96        51.06        65.00 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1632 
        2.99         2.96        18.58        18.02        20.61        56.94 
TCGA-25-1635 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 
       51.22        85.05        13.02        49.05         3.02        12.00 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 
        2.96        29.03        31.00        26.99        44.71        47.18 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1711 
       33.70        31.20        16.90        59.67        41.98        34.62 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1776 TCGA-29-1778 
       85.68        62.93        31.23        22.98        11.84        14.93 
TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 
        8.38         5.36        34.62        86.17        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 
        4.90        42.25        11.84         9.76        21.04        51.91 
TCGA-30-1855 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1887 TCGA-30-1891 
        2.47        48.10        44.91         6.12        24.26        30.05 
TCGA-30-1892 TCGA-31-1946 TCGA-31-1951 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       48.79        30.18        22.49        44.12         2.20        28.77 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-2530 
       21.53        22.55         8.55        25.74        27.85        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2551 
       29.49        29.82        25.08        23.80        21.60        16.18 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-57-1583 
        7.99        26.04        23.74         9.44        40.77        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       21.14        22.32        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2354 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       22.32        34.39        11.11         8.09        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       18.54        27.88        28.47        44.84        35.80         2.43 
TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 
        1.45         5.79        11.41        13.02        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1917 TCGA-61-1998 TCGA-61-2008 TCGA-61-2017 
       42.51        48.92        43.43         5.52        30.64        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2109 
       45.40         4.80         4.77        51.72        61.64        20.68 
TCGA-VG-A8LO 
        0.79 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.26              0.36 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           129.96            180.20 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            25.94             29.03 
[1] "0.3 - 130.0 (25.9)" "0.4 - 180.2 (29.0)"
[1] "hr=" "1.1"
D58V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  9Q LOSS MUTATED         1   275                2
  9Q LOSS WILD-TYPE       1   282                0
D58V3, multiclass
                  clus
vv                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  OMENTUM                        1                 1
  OVARY                        275               282
  PERITONEUM OVARY               2                 0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, continuous
D58V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2 283
  9Q LOSS WILD-TYPE   1 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2  283
  9Q LOSS WILD-TYPE    1  285
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                2                 1
  YES             283               285
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED    8 12  3  2
  9Q LOSS WILD-TYPE  6 14  2  1
D58V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0               8                 6
  R1              12                14
  R2               3                 2
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  1     6
  9Q LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q LOSS MUTATED                          16
  9Q LOSS WILD-TYPE                        16
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           1   233
  9Q LOSS WILD-TYPE                                         0   242
D58V7, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 2
  ASIAN                                                   6                12
  BLACK OR AFRICAN AMERICAN                              16                16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 233               242
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     5 159
  9Q LOSS WILD-TYPE   5 166
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5  159
  9Q LOSS WILD-TYPE    5  166
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 5
  NOT HISPANIC OR LATINO             159               166
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    45  46
  10P LOSS WILD-TYPE 221 244
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                91                465 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                46                244 
$`10P LOSS MUTATED`
TCGA-04-1364 TCGA-04-1371 TCGA-04-1648 TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 
       33.67        82.39        28.64        29.16        57.76        17.98 
TCGA-09-2043 TCGA-09-2053 TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 TCGA-13-0760 
        6.18        39.75        35.44        19.86         2.73        11.54 
TCGA-13-0764 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0889 TCGA-13-0891 
       31.04        30.35         8.12        43.86        61.84        69.01 
TCGA-13-0893 TCGA-13-0904 TCGA-13-0921 TCGA-13-1408 TCGA-13-1484 TCGA-13-1489 
       43.36        48.33         4.64         5.92        98.04        82.88 
TCGA-13-1500 TCGA-13-1507 TCGA-13-2057 TCGA-13-2065 TCGA-20-1684 TCGA-23-1114 
       13.97         4.77        14.24         8.75        19.10        68.68 
TCGA-23-2072 TCGA-23-2078 TCGA-24-0979 TCGA-24-1104 TCGA-24-1416 TCGA-24-1425 
       24.95        87.48        41.56        63.55         6.38         5.95 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1466 TCGA-24-1467 TCGA-24-1471 TCGA-24-1474 
       19.17        43.53        45.14       105.99         1.18        22.22 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1923 
       39.88        19.53        48.33         8.32         3.72        22.68 
TCGA-24-2019 TCGA-24-2026 TCGA-24-2030 TCGA-24-2254 TCGA-24-2280 TCGA-24-2288 
        4.87        34.82        53.95        57.07        70.45         0.82 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1323 TCGA-25-1625 TCGA-25-1632 
       55.86        53.26        26.96        12.00        18.02        56.94 
TCGA-25-2393 TCGA-25-2398 TCGA-25-2399 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       38.04        45.01        19.99        31.20        68.32         0.53 
TCGA-29-1707 TCGA-29-1761 TCGA-29-1769 TCGA-30-1714 TCGA-30-1855 TCGA-31-1944 
       41.98        17.00        22.98        38.07         2.47        45.57 
TCGA-31-1951 TCGA-31-1959 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 
       22.49         2.20        29.49        29.82        25.08        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-42-2589 TCGA-59-A5PD TCGA-61-1734 
       20.98        18.31        20.52        42.02        20.52        28.47 
TCGA-61-1737 TCGA-61-1743 TCGA-61-1913 TCGA-61-1914 TCGA-61-2092 TCGA-61-2094 
       44.84        43.69        48.92        56.61        51.72        71.74 
TCGA-61-2113 
       22.22 

$`10P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 
       63.98        65.46        49.28        32.52        44.32        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       71.47        56.55        41.59        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 
       29.10        84.20        55.43        48.89        27.88        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 TCGA-09-0369 
       36.23        31.86        47.70        45.37         9.47        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
        9.99        38.43        89.33        74.93        41.62        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       61.87        55.36        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 
        8.55        97.55         6.12        35.15         4.54       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       71.11        63.09        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.47        18.51        33.24        32.28        11.70 
TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
        3.91        35.80        15.12         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58        12.39        31.10        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 
        2.50        11.18        11.38        34.06        32.25        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
        8.45        38.93        36.72        28.70        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        7.79         8.28         8.19        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       68.94       107.18        91.40        74.27        66.67        70.39 
TCGA-13-0890 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       67.99        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        14.89        13.81         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 
       10.88         6.61         7.36         6.05         6.84         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.21         5.33        54.64        87.06        61.71        29.42 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       20.68        22.39        70.82        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 
       49.25         4.24        54.31        37.61        38.40        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       16.57         4.21         4.41         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT 
        3.09        12.23         8.61        10.78         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.42        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       25.38        16.70         2.93         2.66        47.54        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        31.76        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.24        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       31.20         4.57        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
        6.38        39.09        33.47        58.13         0.53       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
       91.66        77.00        49.84         2.76         4.70         4.50 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 
        7.63        19.66        11.64        21.80         7.66        22.32 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       54.12        47.41         6.31         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        0.76         6.25         6.02         5.36         4.83        17.39 
TCGA-24-1430 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 
       28.37        18.67         8.55        72.92        12.46         9.11 
TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
        3.45        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       44.09        45.50        47.70        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 
       90.15        88.37        38.24         3.48         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 
       11.28         5.79         5.52         9.80        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 
       11.05        81.11       152.02        44.84        58.16       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 
       14.43        18.48        28.18        64.01        44.52        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 
        0.79         0.36        47.54        31.63        44.61        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 
       36.23        16.64        33.11         1.02        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.99         2.96        18.58        15.81         0.36        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        7.86         0.30        60.59        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       24.99        18.05        85.05        13.02        49.05         1.02 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
        3.02        12.00        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       26.99        78.90        44.71        47.18       101.79        38.53 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
        0.79        33.70        16.90        18.67        59.67        18.25 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       29.23        34.62        85.68        66.81        62.93        39.12 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       31.23        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       12.30        14.93         8.38         7.23         5.36        34.62 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       86.17        65.00        62.47        45.11         4.90        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 
       11.84        11.47         9.76        21.04        51.91        36.26 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       15.68         0.26        48.10        44.91        34.78         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       36.62         1.22        57.57        24.26        30.05        48.79 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 
       30.18        18.77         6.71        42.51        44.12        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       25.74        27.85        24.23        24.69        35.05        33.01 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2543 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       25.91        23.80         2.24        14.17         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
       11.47         7.99        26.04        23.74         9.44         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
       40.77         1.48        24.03        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       22.32        29.00        25.08        25.02       180.20        80.12 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       44.81        11.11         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
       27.88         4.34        31.79        48.79        35.80         2.43 
TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       33.67         1.45         8.42         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 
        9.07        34.13        31.30        37.05        42.51        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       43.43        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       17.98         4.01        30.64        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2095 TCGA-61-2096 
       45.96        45.40         4.80         4.77        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       44.52       125.75         6.35        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         8.05 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.53               0.26 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            105.99             180.20 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             29.49              27.72 
[1] "0.5 - 106.0 (29.5)" "0.3 - 180.2 (27.7)"
[1] "hr=" "1.1"
D59V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10P LOSS MUTATED         0    93                0
  10P LOSS WILD-TYPE       2   464                2
D59V3, multiclass
                  clus
vv                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          93                464
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, continuous
D59V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  95
  10P LOSS WILD-TYPE   2 473
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   95
  10P LOSS WILD-TYPE    2  473
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 1                  2
  YES               95                473
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  10P LOSS MUTATED    4  4  0  0
  10P LOSS WILD-TYPE 10 22  5  3
D59V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0                4                 10
  R1                4                 22
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     2
  10P LOSS WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P LOSS MUTATED                           5
  10P LOSS WILD-TYPE                        27
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           1    77
  10P LOSS WILD-TYPE                                         0   398
D59V7, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                5                 27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                   77                398
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  46
  10P LOSS WILD-TYPE   9 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   46
  10P LOSS WILD-TYPE    9  279
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               46                279
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    59  60
  10Q LOSS WILD-TYPE 207 230
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               119                437 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                60                230 
$`10Q LOSS MUTATED`
TCGA-04-1343 TCGA-04-1364 TCGA-04-1648 TCGA-04-1649 TCGA-09-0364 TCGA-09-0366 
       11.87        33.67        28.64        64.64        29.16        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1667 TCGA-09-1673 TCGA-09-2043 TCGA-09-2053 
       17.98        35.57        61.87         3.02         6.18        39.75 
TCGA-10-0935 TCGA-10-0938 TCGA-13-0724 TCGA-13-0751 TCGA-13-0760 TCGA-13-0764 
       35.44        19.86         2.73        55.17        11.54        31.04 
TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0807 TCGA-13-0889 TCGA-13-0891 
       30.35         8.12        43.86        13.61        61.84        69.01 
TCGA-13-0893 TCGA-13-0899 TCGA-13-0904 TCGA-13-0911 TCGA-13-0916 TCGA-13-0921 
       43.36        56.15        48.33        27.72        21.17         4.64 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1489 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 
        6.05         5.92        82.88        73.55         4.24        54.31 
TCGA-13-1507 TCGA-13-2057 TCGA-13-2065 TCGA-20-1684 TCGA-20-1686 TCGA-23-1114 
        4.77        14.24         8.75        19.10         2.93        68.68 
TCGA-23-2072 TCGA-24-0979 TCGA-24-1104 TCGA-24-1416 TCGA-24-1418 TCGA-24-1430 
       24.95        41.56        63.55         6.38         7.99        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 
       19.17        18.67        43.53         8.55        45.14       105.99 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1557 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 
        1.18        22.22        39.88        48.33         8.32         3.72 
TCGA-24-1850 TCGA-24-1928 TCGA-24-2026 TCGA-24-2030 TCGA-24-2254 TCGA-24-2280 
        5.52        11.05        34.82        53.95        57.07        70.45 
TCGA-24-2288 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1320 TCGA-25-1323 
        0.82        55.86        53.26        26.96        36.95        12.00 
TCGA-25-1632 TCGA-25-1635 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-29-1697 
       56.94        51.22        45.01        19.99        42.02        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1761 TCGA-29-1766 
       68.32         0.53        16.90        59.67        17.00        39.12 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1778 TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 
       22.98        24.36        14.93        38.07         2.47        15.68 
TCGA-30-1859 TCGA-31-1944 TCGA-31-1951 TCGA-31-1953 TCGA-31-1959 TCGA-36-1577 
       48.10        45.57        22.49         6.71         2.20        25.74 
TCGA-36-1581 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 
       24.69        29.49        29.82        25.08        21.60         2.24 
TCGA-36-2545 TCGA-36-2547 TCGA-42-2589 TCGA-61-1728 TCGA-61-1734 TCGA-61-1737 
       18.31        20.52        42.02        27.88        28.47        44.84 
TCGA-61-1743 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 TCGA-61-2012 TCGA-61-2088 
       43.69        48.92        56.61        15.75        30.64         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2102 TCGA-61-2113 TCGA-OY-A56P 
       51.72        71.74         6.48        22.22        39.68 

$`10Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       18.51        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 
       65.46        49.28        32.52        44.32        76.57        71.47 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       82.39        56.55        41.59        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 
       29.10        84.20        55.43        48.89        27.88        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 TCGA-09-1659 TCGA-09-1661 
       31.86        47.70        45.37         9.47         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 
       89.33        74.93        41.62        57.60        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
       17.98         5.85         8.55        97.55         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 
        4.54       112.41        71.11        63.09        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        54.31        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 
       32.28        11.70         3.91        35.80        15.12         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       24.59        44.55        39.58        12.39        31.10        15.19 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 
       17.82         2.50        11.18        11.38        34.06        32.25 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       21.40         8.45        38.93        36.72        28.70        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
        8.71         7.79         8.28         8.19        35.28        35.28 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       68.94       107.18        91.40        74.27        66.67        70.39 
TCGA-13-0890 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 
       67.99        57.47        57.07        19.36        47.38        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 
       44.94        44.84        37.08        34.06        29.98        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       61.71        29.42        98.04        20.68        22.39        70.82 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       52.44        38.20        49.25        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 
       32.84        16.57         4.21         4.41         4.18         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 
        3.91         3.09        12.23         8.61        10.78         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       54.77         8.42        23.05        25.94        26.20        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       27.52        25.38        16.70         2.66        47.54        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        31.76        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.24        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       31.20         4.57        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
        6.38        39.09        33.47        58.13         0.53       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       87.48        91.66        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 
        4.50         7.63        19.66        11.64        21.80         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1419 
       22.32        54.12        47.41         6.31         7.82         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1428 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 
       17.39        72.92        12.46         9.11         3.45        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       57.40        64.27        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 
       41.39        58.09        88.50        70.62        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       88.37        38.24         3.48         3.81         4.37        11.28 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 
        5.79         9.80        22.68        30.21        16.44        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
        4.87       152.02        44.84        58.16       109.71        14.43 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 
       18.48        28.18        64.01        44.52        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 
        0.36        47.54        31.63        44.61        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       16.64        33.11         1.02        32.02        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 
        1.02        34.98        65.00        33.96         2.99         2.96 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       18.58        18.02        15.81         0.36        20.61         7.86 
TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
        0.30        60.59        35.54        14.96        24.99        18.05 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       85.05        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2397 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       12.00         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       44.71        47.18       101.79        38.53         0.79        33.70 
TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 
       18.67        18.25        41.98        29.23        34.62        85.68 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       66.81        62.93        31.23        22.55        17.33        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       11.84        12.30         8.38         7.23         5.36        34.62 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       86.17        65.00        62.47        45.11         4.90        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 
       11.84        11.47         9.76        21.04        51.91        36.26 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
        0.26        44.91        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1950 
       57.57        24.26        30.05        48.79        30.18        18.77 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       42.51        44.12        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 
       22.55         8.55        30.08        27.85        24.23        35.05 
TCGA-36-2530 TCGA-36-2537 TCGA-36-2540 TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 
       33.01        25.91        23.80        20.98        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       16.18        11.47         7.99        26.04        23.74         9.44 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
        7.46        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.74        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
        5.42        44.81        20.52        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 
       31.43        18.54         4.34        31.79        48.79        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
        2.43        33.67         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       13.02         9.07        34.13        31.30        37.05        42.51 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       67.76        43.43        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 
       17.98         4.01        30.64        39.85         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       45.40         4.80        61.64        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2612 
       55.50        76.87        20.68        44.52       125.75         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61        18.94         0.79         8.05 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.53               0.26 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            105.99             180.20 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             28.37              27.88 
[1] "0.5 - 106.0 (28.4)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1"  
D60V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  10Q LOSS MUTATED         0   119                1
  10Q LOSS WILD-TYPE       2   438                1
D60V3, multiclass
                  clus
vv                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  OMENTUM                         0                  2
  OVARY                         119                438
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, continuous
D60V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3 121
  10Q LOSS WILD-TYPE   0 447
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3  121
  10Q LOSS WILD-TYPE    0  447
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 3                  0
  YES              121                447
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS MUTATED    4  6  1  0
  10Q LOSS WILD-TYPE 10 20  4  3
D60V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0                4                 10
  R1                6                 20
  R2                1                  4
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     4
  10Q LOSS WILD-TYPE                                3    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q LOSS MUTATED                           6
  10Q LOSS WILD-TYPE                        26
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           1   102
  10Q LOSS WILD-TYPE                                         0   373
D60V7, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                                6                 26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  102                373
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  65
  10Q LOSS WILD-TYPE   9 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   65
  10Q LOSS WILD-TYPE    9  260
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               65                260
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    87 102
  11P LOSS WILD-TYPE 179 188
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               189                367 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               102                188 
$`11P LOSS MUTATED`
TCGA-04-1331 TCGA-04-1338 TCGA-04-1347 TCGA-04-1351 TCGA-04-1356 TCGA-04-1367 
       40.24        46.62        63.09        65.46        49.28        71.47 
TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       19.99        29.10        84.20        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1655 TCGA-09-0366 TCGA-09-1659 TCGA-09-1661 TCGA-09-1666 
       64.64        45.37        57.76         9.99        38.43        57.60 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1674 TCGA-09-2053 TCGA-10-0926 
       61.87        55.36        17.98         8.55        39.75        25.91 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0937 TCGA-10-0938 TCGA-13-0723 TCGA-13-0751 
       18.51        33.24        15.12        19.86        39.58        55.17 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0802 
       11.38        11.54        32.25        31.04         8.45         8.19 
TCGA-13-0804 TCGA-13-0886 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 
       35.28        74.27        56.15        57.07        19.36        48.33 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 TCGA-13-1404 
       44.94        44.84        29.98        13.81         4.64         6.61 
TCGA-13-1409 TCGA-13-1411 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        6.84         4.21        54.64        61.71        29.42        98.04 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1494 TCGA-13-1495 TCGA-13-1500 TCGA-13-1505 
       22.39        82.88        38.20        49.25        13.97         4.21 
TCGA-13-1507 TCGA-13-1512 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 
        4.77         3.09         8.61         8.75         8.42        25.94 
TCGA-20-0991 TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1027 
       26.20        25.38         2.93         2.66        42.54        31.76 
TCGA-23-1031 TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 TCGA-23-1122 TCGA-23-2077 
       18.90        31.20        68.68        86.01        39.09       115.89 
TCGA-23-2643 TCGA-24-0968 TCGA-24-0970 TCGA-24-1105 TCGA-24-1418 TCGA-24-1427 
        4.70        19.66        11.64        47.41         7.99         4.83 
TCGA-24-1428 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1474 TCGA-24-1544 
       17.39         8.55        72.92        45.14        22.22        26.96 
TCGA-24-1545 TCGA-24-1549 TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1846 
       57.40        56.58        45.50        47.70        17.23         4.37 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 TCGA-24-2026 TCGA-24-2027 
       22.68        30.21        81.11         4.87        34.82       109.71 
TCGA-24-2029 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 
       14.43        57.07        36.16         0.79        47.54        70.45 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       16.64        33.11        53.26        34.98        65.00        36.95 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1634 
       12.00         2.96        20.61         7.86         0.30        35.54 
TCGA-25-1870 TCGA-25-1871 TCGA-25-2392 TCGA-25-2393 TCGA-29-1688 TCGA-29-1695 
       14.96        24.99         1.02        38.04        78.90         0.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1702 TCGA-29-1703 TCGA-29-1711 
       33.70        31.20        68.32        18.67        59.67        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 
       17.00        85.68        66.81        62.93        22.98        24.36 
TCGA-29-1777 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2434 TCGA-30-1853 
       12.30        86.17        65.00        45.11        11.47        36.26 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1887 TCGA-31-1950 TCGA-31-1953 TCGA-36-1569 
       34.78        36.62        24.26        18.77         6.71        29.10 
TCGA-36-1577 TCGA-36-1581 TCGA-36-2529 TCGA-36-2538 TCGA-36-2543 TCGA-36-2549 
       25.74        24.69        35.05        25.08         2.24         6.05 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2589 TCGA-57-1582 TCGA-57-1993 TCGA-59-2352 
       11.47         7.99        42.02        24.03        25.08         9.40 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 
       44.81         8.09        20.94        31.43        27.88         4.34 
TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 
       31.79        35.80        33.67         9.07        34.13        37.05 
TCGA-61-1917 TCGA-61-1919 TCGA-61-2002 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 
       43.43        38.17        17.98        45.40         4.77        51.72 
TCGA-61-2094 TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 
       71.74         6.48       125.75        22.22         6.35         8.61 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         8.05 

$`11P LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       41.00         1.81        49.15         2.01        18.51        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 
       65.52        48.76        21.57        63.98        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 
       33.67        76.57        82.39        56.55        41.59        38.37 
TCGA-04-1530 TCGA-04-1638 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 
      119.08        55.43        36.23        31.86        47.70        29.16 
TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
        9.47        17.98        35.57        89.33        74.93        41.62 
TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       30.51         5.85         3.02        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 
       35.15         4.54       112.41        71.11        63.09        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 
       26.93        12.46        54.31        81.47        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
        3.91        35.44        35.80         6.21        24.59        44.55 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 
        2.73        12.39        31.10        15.19        17.82         2.50 
TCGA-13-0757 TCGA-13-0761 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       11.18        34.06        21.40        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       30.35        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       43.86        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       66.67        70.39        61.84        67.99        69.01        43.36 
TCGA-13-0897 TCGA-13-0903 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       57.47        47.38        47.84        37.08        27.72        34.06 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 
       21.17        14.89         6.41         6.08        10.88         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 TCGA-13-1481 TCGA-13-1485 
        6.05         5.92         4.70         5.33        87.06        20.68 
TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       70.82        52.44        73.55         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 
       38.40        32.84        16.57         4.41         4.18         2.56 
TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT 
        3.91        14.24        12.23        10.78         6.28        54.77 
TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 
       23.05        72.20        27.52        19.10        16.70        47.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        15.39        26.83        49.41         8.81        29.13 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 
        2.24        51.35        54.51         3.22         4.57        33.30 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
      129.96         4.27         6.38        33.47        58.13         0.53 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       24.95        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        4.50         7.63        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 
       54.12        63.55         6.31         6.38         7.82         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 
        0.76         6.25         6.02         5.95         5.36        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 
       19.17        18.67        43.53        12.46       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 
        3.45         1.18        64.27        16.21        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       44.09        25.87        10.26        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 
       38.24         8.32         3.48         3.72         3.81        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1927 TCGA-24-1928 TCGA-24-2020 
        5.79         5.52         9.80        16.44        11.05       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       44.84        58.16        53.95        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       44.52         0.36        31.63        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       36.23        55.86         1.02        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1321 TCGA-25-1322 TCGA-25-1623 TCGA-25-1625 
       37.02         1.02        33.96         2.99        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1877 
       15.81         0.36        56.94        60.59        51.22        18.05 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       85.05        13.02        49.05         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1699 TCGA-29-1701 
       44.71        47.18       101.79        38.53         0.53        16.90 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 
       18.25        41.98        29.23        39.12        31.23        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       17.33        12.36        11.84        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
        5.36        34.62        62.47         4.90        42.25        11.84 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
        9.76        21.04        38.07        51.91         2.47        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 
        0.26        48.10        44.91         6.12         1.22        57.57 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1955 
       30.05        48.79        45.57        30.18        22.49        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       44.12         2.20        28.77        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 
        8.55        30.08        27.85        24.23        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 
       29.82        25.91        23.80        21.60        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       20.52        14.17        16.18        26.04        23.74         9.44 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 
        7.46        40.77         1.48        11.38        21.14         1.74 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       22.32        29.00        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1721 
      116.12        34.39         2.14         5.42        20.52        11.11 
TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1743 
       18.54        28.47        48.79        44.84         2.43        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 
        1.45         8.42         5.79        11.41        13.02        31.30 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 
       42.51        48.92        56.61        67.76        15.75         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
        5.52        14.50         4.01        30.64        39.85        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
        1.18        45.96         4.80        61.64        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2613 
       65.52        55.50        76.87        20.68        44.52        31.07 
TCGA-OY-A56P 
       39.68 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.30               0.26 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            125.75             180.20 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             29.42              26.99 
[1] "0.3 - 125.8 (29.4)" "0.3 - 180.2 (27.0)"
[1] "hr=" "1"  
D61V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  11P LOSS MUTATED         1   190                1
  11P LOSS WILD-TYPE       1   367                1
D61V3, multiclass
                  clus
vv                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         190                367
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, continuous
D61V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     1 195
  11P LOSS WILD-TYPE   2 373
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1  195
  11P LOSS WILD-TYPE    2  373
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 1                  2
  YES              195                373
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  11P LOSS MUTATED    6  9  2  2
  11P LOSS WILD-TYPE  8 17  3  1
D61V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                6                  8
  R1                9                 17
  R2                2                  3
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     5
  11P LOSS WILD-TYPE                                3    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P LOSS MUTATED                          15
  11P LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           0   162
  11P LOSS WILD-TYPE                                         1   313
D61V7, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    5                 13
  BLACK OR AFRICAN AMERICAN                               15                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  162                313
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2 103
  11P LOSS WILD-TYPE   8 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2  103
  11P LOSS WILD-TYPE    8  222
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO              103                222
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    65  79
  11Q LOSS WILD-TYPE 201 211
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               144                412 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                79                211 
$`11Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1338 TCGA-04-1356 TCGA-04-1367 TCGA-04-1517 TCGA-04-1536 
       40.24        46.62        49.28        71.47        19.99        29.10 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1655 TCGA-09-0366 TCGA-09-1666 TCGA-09-1670 
       28.64        64.64        45.37        57.76        57.60        17.98 
TCGA-09-2051 TCGA-09-2053 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0937 
       63.09        39.75        25.91        18.51        33.24        15.12 
TCGA-10-0938 TCGA-13-0723 TCGA-13-0724 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
       19.86        39.58         2.73        17.82        55.17        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0768 TCGA-13-0795 TCGA-13-0804 
       11.38        11.54        32.25         8.45        19.59        35.28 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0920 
       56.15        57.07        48.33        44.94        44.84        13.81 
TCGA-13-0921 TCGA-13-1404 TCGA-13-1409 TCGA-13-1411 TCGA-13-1477 TCGA-13-1482 
        4.64         6.61         6.84         4.21        54.64        61.71 
TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 TCGA-13-1494 TCGA-13-1495 TCGA-13-1501 
       29.42        22.39        82.88        38.20        49.25        32.84 
TCGA-13-1505 TCGA-13-1512 TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0991 
        4.21         3.09         8.61         8.75         8.42        26.20 
TCGA-20-1683 TCGA-20-1686 TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 TCGA-23-1122 
       25.38         2.93        31.20        68.68        86.01        39.09 
TCGA-23-2077 TCGA-24-0968 TCGA-24-0970 TCGA-24-0982 TCGA-24-1105 TCGA-24-1428 
      115.89        19.66        11.64        22.32        47.41        17.39 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1544 TCGA-24-1562 TCGA-24-1567 TCGA-24-1923 
       72.92        45.14        26.96        45.50        17.23        22.68 
TCGA-24-1924 TCGA-24-2019 TCGA-24-2026 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
       30.21         4.87        34.82        57.07        36.16         0.79 
TCGA-24-2280 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1319 TCGA-25-1320 
       70.45        16.64        33.11        53.26        65.00        36.95 
TCGA-25-1321 TCGA-25-1329 TCGA-25-1628 TCGA-25-1870 TCGA-25-1871 TCGA-25-2392 
       33.96         2.96        20.61        14.96        24.99         1.02 
TCGA-25-2393 TCGA-29-1688 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
       38.04        78.90         0.79        33.70        31.20        68.32 
TCGA-29-1703 TCGA-29-1711 TCGA-29-1761 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 
       59.67        34.62        17.00        22.98        24.36        12.36 
TCGA-29-1777 TCGA-29-2414 TCGA-29-2428 TCGA-29-2434 TCGA-30-1853 TCGA-30-1861 
       12.30        86.17        45.11        11.47        36.26        34.78 
TCGA-30-1866 TCGA-31-1953 TCGA-36-1571 TCGA-36-1581 TCGA-36-2529 TCGA-36-2538 
       36.62         6.71        22.85        24.69        35.05        25.08 
TCGA-36-2543 TCGA-36-2549 TCGA-36-2552 TCGA-42-2589 TCGA-57-1582 TCGA-57-1993 
        2.24         6.05        11.47        42.02        24.03        25.08 
TCGA-59-2348 TCGA-59-2352 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 
      180.20         9.40        20.94        31.43        27.88         4.34 
TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1904 TCGA-61-1910 
       31.79        35.80        33.67        43.69         9.07        37.05 
TCGA-61-1911 TCGA-61-1917 TCGA-61-1919 TCGA-61-2012 TCGA-61-2018 TCGA-61-2092 
       42.51        43.43        38.17        30.64        45.40        51.72 
TCGA-61-2102 TCGA-61-2111 TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56Q TCGA-WR-A838 
        6.48       125.75        22.22         8.61        18.94         8.05 

$`11Q LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       41.00         1.81        49.15         2.01        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       65.52        63.09        48.76        21.57        63.98        65.46 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 
       32.52        44.32        33.67        76.57        82.39        56.55 
TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       41.59        38.37       119.08        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 
       27.88        36.23        31.86        47.70        29.16         9.47 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       17.98        35.57         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 
       41.62        61.87        55.36        30.51         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        8.55        97.55         6.18         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
      112.41        71.11        20.94        26.93        12.46        54.31 
TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       81.47        32.28        11.70         3.91        35.44        35.80 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
        6.21        24.59        44.55        12.39        31.10        15.19 
TCGA-13-0755 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 
        2.50        34.06        31.04        21.40        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       28.70        30.35         8.71         7.79         8.12         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
        8.19        43.86        35.28        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       91.40        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 
       69.01        43.36        57.47        19.36        47.38        47.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       37.08        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        6.41         6.08        10.88         7.36         6.05         5.92 
TCGA-13-1410 TCGA-13-1412 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 
        4.70         5.33        87.06        98.04        20.68        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       52.44        73.55         4.24        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       13.97        16.57         4.41         4.77         4.18         2.56 
TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT 
        3.91        14.24        12.23        10.78         6.28        54.77 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
       23.05        25.94        72.20        27.52        19.10        16.70 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.66        47.54        42.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       31.76        49.41         8.81        29.13        18.90         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 
       51.35        54.51         3.22         4.57        33.30       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        4.27         6.38        33.47        58.13         0.53        24.95 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       87.48        91.66        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
        4.50         7.63        21.80        41.56         7.66        54.12 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       63.55         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 
        0.76         6.25         6.02         5.95         5.36         4.83 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 
       28.37        19.17        18.67        43.53         8.55        12.46 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 
      105.99         9.11         3.45         1.18        22.22        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       47.70        25.87        10.26        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       38.24         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1927 TCGA-24-1928 
       11.28         5.79         5.52         9.80        16.44        11.05 
TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
       81.11       152.02        44.84        58.16       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 
       53.95        18.48        28.18        64.01        44.52         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       47.54        31.63        44.61         0.82        67.36        36.23 
TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86         1.02        26.96        32.02        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 
        1.02        34.98         2.99        12.00        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       15.81         0.36         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       35.54        51.22        18.05        85.05        13.02        49.05 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 
        3.02        12.00        45.01        19.99        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
       29.03        31.00        26.99        44.71        47.18       101.79 
TCGA-29-1694 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 
       38.53         0.53        16.90        18.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       29.23        85.68        66.81        62.93        39.12        31.23 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       22.55        17.33        11.84        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 
        5.36        34.62        65.00        62.47         4.90        42.25 
TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       11.84         9.76        21.04        38.07        51.91         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 
       15.68         0.26        48.10        44.91         6.12         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       57.57        24.26        30.05        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       18.77        22.49        42.51        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       29.10        21.53        22.55         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       27.85        24.23        33.01        29.49        29.82        25.91 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       23.80        21.60        20.98        18.31        20.52        14.17 
TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
       16.18         7.99        26.04        23.74         9.44         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
       40.77         1.48        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 
       29.00        25.02        80.12        22.32       116.12        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 
        2.14         5.42        44.81        20.52        11.11         8.09 
TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1895 
       18.54        28.47        48.79        44.84         2.43         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 
        8.42         5.79        11.41        13.02        34.13        31.30 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        67.76        15.75         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 
       14.50        17.98         4.01        30.64        39.85         1.18 
TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.96         4.80         4.77        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        65.52        55.50        76.87        20.68        44.52 
TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-VG-A8LO 
        6.35        31.07        39.68         0.79 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.79               0.26 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            180.20             152.02 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            30.425             27.255 
[1] "0.8 - 180.2 (30.4)" "0.3 - 152.0 (27.3)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  11Q LOSS MUTATED         1   144                1
  11Q LOSS WILD-TYPE       1   413                1
D62V3, multiclass
                  clus
vv                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         144                413
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, continuous
D62V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1 147
  11Q LOSS WILD-TYPE   2 421
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1  147
  11Q LOSS WILD-TYPE    2  421
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 1                  2
  YES              147                421
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS MUTATED    5  6  1  1
  11Q LOSS WILD-TYPE  9 20  4  2
D62V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                5                  9
  R1                6                 20
  R2                1                  4
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q LOSS MUTATED                          10
  11Q LOSS WILD-TYPE                        22
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           0   127
  11Q LOSS WILD-TYPE                                         1   348
D62V7, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                               10                 22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  127                348
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3  77
  11Q LOSS WILD-TYPE   7 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   77
  11Q LOSS WILD-TYPE    7  248
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  7
  NOT HISPANIC OR LATINO               77                248
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    37  40
  12P LOSS WILD-TYPE 229 250
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                77                479 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                40                250 
$`12P LOSS MUTATED`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1364 TCGA-04-1638 TCGA-09-1667 
        1.81        49.15         2.01        33.67        55.43        61.87 
TCGA-09-1675 TCGA-09-2044 TCGA-10-0936 TCGA-13-0724 TCGA-13-0755 TCGA-13-0758 
       97.55         6.12        35.80         2.73         2.50        11.38 
TCGA-13-0766 TCGA-13-0793 TCGA-13-0803 TCGA-13-0807 TCGA-13-0885 TCGA-13-0891 
       21.40        28.70        43.86        13.61        91.40        69.01 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0919 TCGA-13-1403 TCGA-13-1405 TCGA-13-1483 
       47.84        44.84        14.89        10.88         7.36        29.42 
TCGA-13-1488 TCGA-13-1494 TCGA-13-1497 TCGA-13-1501 TCGA-13-1507 TCGA-13-1512 
       70.82        38.20        54.31        32.84         4.77         3.09 
TCGA-20-0987 TCGA-20-1685 TCGA-23-1120 TCGA-23-1122 TCGA-23-2072 TCGA-23-2078 
       23.05        16.70         4.27        39.09        24.95        87.48 
TCGA-24-0979 TCGA-24-1105 TCGA-24-1425 TCGA-24-1428 TCGA-24-1435 TCGA-24-1471 
       41.56        47.41         5.95        17.39        43.53         1.18 
TCGA-24-1550 TCGA-24-1849 TCGA-24-2026 TCGA-24-2036 TCGA-24-2280 TCGA-24-2297 
       41.06         5.79        34.82        64.01        70.45        55.86 
TCGA-25-1320 TCGA-25-1632 TCGA-25-2397 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 
       36.95        56.94        12.00        29.03        26.99        78.90 
TCGA-29-1691 TCGA-29-1703 TCGA-29-1711 TCGA-29-1764 TCGA-29-1776 TCGA-29-2432 
       47.18        59.67        34.62        62.93        11.84        11.84 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 TCGA-36-2538 TCGA-36-2549 
       51.91        36.26         0.26        34.78        25.08         6.05 
TCGA-57-1585 TCGA-59-A5PD TCGA-61-1727 TCGA-61-1734 TCGA-61-1738 TCGA-61-1903 
        1.74        20.52        18.54        28.47        35.80        13.02 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1919 TCGA-61-2008 TCGA-61-2102 
       37.05        48.92        38.17        30.64         6.48 

$`12P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       40.24        41.00        46.62        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       63.09        48.76        21.57        63.98        65.46        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       32.52        44.32        76.57        71.47        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       41.59        19.99        38.37       119.08        29.10        84.20 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       47.70        45.37        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       35.57         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       57.60        55.36        30.51        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        8.55         6.18        35.15         4.54       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       63.09        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.47        18.51        33.24        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        3.91        35.44        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58        12.39        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       55.17        11.18        11.54        34.06        32.25        31.04 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
        8.45        38.93        36.72        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
        7.79         8.12         8.28         8.19        35.28        35.28 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       68.94       107.18        74.27        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       67.99        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.38        48.33        44.94        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        13.81         4.64         6.41         6.08 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        6.61         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 
        5.33        54.64        87.06        61.71        98.04        20.68 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 
       22.39        82.88        52.44        73.55        49.25         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        13.97        16.57         4.21         4.41 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.91        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 
       10.78         8.75         6.28        54.77         8.42        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 
       26.20        72.20        27.52        25.38        19.10         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.66        47.54        42.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       31.76        49.41         8.81        29.13        18.90         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
       51.35        54.51         3.22        31.20        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 
       33.30        86.01       129.96         6.38        33.47        58.13 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
        0.53       115.89        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.70         4.50         7.63        19.66        11.64        21.80 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 
        7.66        22.32        54.12        63.55         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        7.82         7.99         7.86         0.76         6.25         6.02 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        5.36         4.83        28.37        19.17        18.67         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       72.92        12.46        45.14       105.99         9.11         3.45 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       51.91        41.39        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 
        3.48         3.72         3.81         4.37        11.28         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        9.80        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
        4.87       152.02        44.84        58.16       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       53.95        18.48        28.18        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 
        0.79         0.36        47.54        31.63        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 
       67.36        36.23        16.64        33.11        53.26         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        32.02        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       65.00        33.96         2.99        12.00         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.02        15.81         0.36        20.61         7.86         0.30 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       60.59        35.54        51.22        14.96        24.99        18.05 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       85.05        13.02        49.05         1.02        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 TCGA-29-1690 
       45.01        19.99        42.02         2.96        31.00        44.71 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
        0.53        16.90        18.67        18.25        41.98        29.23 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
       17.00        85.68        66.81        39.12        31.23        22.98 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 
       24.36        22.55        17.33        12.36        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
        8.38         7.23         5.36        34.62        86.17        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 
       62.47        45.11         4.90        42.25        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 
       21.04        38.07         2.47        15.68        48.10        44.91 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
        6.12        36.62         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       48.79        45.57        30.18        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       42.51        44.12         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       24.23        24.69        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.91        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 
       20.52        14.17        16.18        11.47         7.99        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74         9.44        42.02         7.46        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       24.03        11.38        21.14        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.02       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
       34.39         2.14         5.42        44.81        11.11         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
       20.94        31.43        27.88         4.34        31.79        48.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       44.84         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 
        5.79        11.41         9.07        34.13        31.30        42.51 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       56.61        67.76        43.43        15.75         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       14.50        17.98         4.01        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       45.96        45.40         4.80         4.77        51.72        71.74 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 
       61.64        58.39        60.62        65.52        55.50        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       20.68        44.52       125.75        22.22         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        8.61        39.68        18.94         0.79         8.05 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.26               0.30 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             97.55             180.20 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             32.84              26.96 
[1] "0.3 - 97.5 (32.8)"  "0.3 - 180.2 (27.0)"
[1] "hr=" "1"  
D63V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  12P LOSS MUTATED         0    77                0
  12P LOSS WILD-TYPE       2   480                2
D63V3, multiclass
                  clus
vv                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          77                480
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V4, continuous
D63V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  78
  12P LOSS WILD-TYPE   3 490
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   78
  12P LOSS WILD-TYPE    3  490
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 0                  3
  YES               78                490
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  12P LOSS MUTATED    1  3  0  0
  12P LOSS WILD-TYPE 13 23  5  3
D63V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0                1                 13
  R1                3                 23
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  1     2
  12P LOSS WILD-TYPE                                2    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P LOSS MUTATED                           8
  12P LOSS WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           0    63
  12P LOSS WILD-TYPE                                         1   412
D63V7, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                8                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   63                412
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  49
  12P LOSS WILD-TYPE   9 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   49
  12P LOSS WILD-TYPE    9  276
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               49                276
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    50  50
  12Q LOSS WILD-TYPE 216 240
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               100                456 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                50                240 
$`12Q LOSS MUTATED`
TCGA-04-1335 TCGA-04-1356 TCGA-04-1371 TCGA-04-1542 TCGA-04-1638 TCGA-09-1659 
        1.81        49.28        82.39        84.20        55.43         9.99 
TCGA-09-1667 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-13-0724 TCGA-13-0751 
       61.87         8.55        97.55         6.12         2.73        55.17 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0766 TCGA-13-0793 TCGA-13-0803 
        2.50        11.38        11.54        21.40        28.70        43.86 
TCGA-13-0807 TCGA-13-0885 TCGA-13-0891 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 
       13.61        91.40        69.01        48.33        47.84        44.84 
TCGA-13-0919 TCGA-13-0923 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1483 
       14.89         6.41         7.36         5.92         4.21        29.42 
TCGA-13-1489 TCGA-13-1497 TCGA-13-1501 TCGA-13-1507 TCGA-13-1512 TCGA-13-2059 
       82.88        54.31        32.84         4.77         3.09        12.23 
TCGA-20-0987 TCGA-23-1120 TCGA-23-1122 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
       23.05         4.27        39.09        24.95       115.89        87.48 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1425 TCGA-24-1428 
        7.66        22.32        63.55        47.41         5.95        17.39 
TCGA-24-1431 TCGA-24-1471 TCGA-24-1550 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 
       19.17         1.18        41.06        88.37        48.33         8.32 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1927 TCGA-24-2023 TCGA-24-2026 TCGA-24-2036 
        5.79         9.80        16.44        44.84        34.82        64.01 
TCGA-24-2254 TCGA-24-2280 TCGA-24-2297 TCGA-25-1314 TCGA-25-1320 TCGA-25-1632 
       57.07        70.45        55.86        32.02        36.95        56.94 
TCGA-25-1877 TCGA-25-2397 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1703 
       18.05        12.00        26.99        78.90        47.18        59.67 
TCGA-29-1711 TCGA-29-1776 TCGA-29-2427 TCGA-29-2432 TCGA-30-1718 TCGA-30-1853 
       34.62        11.84        62.47        11.84        51.91        36.26 
TCGA-30-1857 TCGA-30-1861 TCGA-30-1891 TCGA-31-1956 TCGA-36-2538 TCGA-36-2549 
        0.26        34.78        30.05        44.12        25.08         6.05 
TCGA-3P-A9WA TCGA-57-1585 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1727 TCGA-61-1734 
        7.99         1.74         5.42        20.52        18.54        28.47 
TCGA-61-1738 TCGA-61-1895 TCGA-61-1903 TCGA-61-1904 TCGA-61-1913 TCGA-61-1917 
       35.80         1.45        13.02         9.07        48.92        43.43 
TCGA-61-1919 TCGA-61-2008 TCGA-61-2087 TCGA-61-2104 
       38.17        30.64         4.80        76.87 

$`12Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       65.46        32.52        44.32        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       56.55        41.59        19.99        38.37       119.08        29.10 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       47.70        45.37        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       35.57        38.43        89.33        74.93        41.62        57.60 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-2043 
       55.36        30.51        17.98         5.85         3.02         6.18 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       35.15         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        54.31        25.91        81.47 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       18.51        33.24        32.28        11.70         3.91        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.80        15.12        19.86         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 
       39.58        12.39        31.10        15.19        17.82        11.18 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       34.06        32.25        31.04         8.45        38.93        36.72 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       30.35        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 
        8.19        35.28        35.28        68.94       107.18        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 
       66.67        70.39        61.84        67.99        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 TCGA-13-0910 
       56.15        57.07        19.36        47.38        44.94        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 
       27.72        34.06        29.98        21.17        13.81         4.64 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 
        6.08        10.88         6.61         6.05         6.84         4.70 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 
        5.33        54.64        87.06        61.71        98.04        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       22.39        70.82        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 
        4.24        37.61        38.40        13.97        16.57         4.21 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 
        4.41         4.18         2.56         3.91        14.24         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 
       10.78         8.75         6.28        54.77         8.42        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       26.20        72.20        27.52        25.38        19.10        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
        2.93         2.66        47.54        42.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        31.76        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
        2.24        51.35        54.51         3.22        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 
        4.57        33.30        86.01       129.96         6.38        33.47 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       58.13         0.53        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.70         4.50         7.63        19.66        11.64        21.80 
TCGA-24-0979 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 
       41.56        54.12         6.31         6.38         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 
        7.86         0.76         6.25         6.02         5.36         4.83 
TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       28.37        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 
       45.14       105.99         9.11         3.45        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        16.21        56.58        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 
       45.50        47.70        25.87        10.26        17.23        90.15 
TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       38.24         3.48         3.72         3.81         4.37        11.28 
TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
        5.52        22.68        30.21        11.05        81.11         4.87 
TCGA-24-2020 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
      152.02        58.16       109.71        14.43        53.95        18.48 
TCGA-24-2035 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       28.18        44.52        36.16         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       31.63        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 
       33.11        53.26         1.02        26.96        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
        1.02        34.98        65.00        33.96         2.99        12.00 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
        2.96        18.58        18.02        15.81         0.36        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        7.86         0.30        60.59        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       24.99        85.05        13.02        49.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
        3.02        45.01        19.99        42.02         2.96        29.03 
TCGA-25-2408 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       31.00        44.71       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 
       31.20        68.32         0.53        16.90        18.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       41.98        29.23        17.00        85.68        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.12        31.23        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        12.30        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       34.62        86.17        65.00        45.11         4.90        42.25 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 
       11.47         9.76        21.04        38.07         2.47        15.68 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       48.10        44.91         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       24.26        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
        6.71        42.51         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       22.85        22.55         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       24.23        24.69        35.05        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.91        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 
       20.52        14.17        16.18        11.47        26.04        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
        9.44        42.02         7.46        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       11.38        21.14        22.32        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
      180.20        80.12        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        2.14        44.81        11.11         8.09        20.94        31.43 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 
       27.88         4.34        31.79        48.79        44.84         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 
       33.67        43.69         8.42         5.79        11.41        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 
       31.30        37.05        42.51        56.61        67.76        15.75 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 
        2.01         5.52        14.50        17.98         4.01        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 TCGA-61-2092 
       30.64         1.18        45.96        45.40         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
        6.48        20.68        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61        39.68        18.94         0.79         8.05 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.26               0.30 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            115.89             180.20 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            29.060             27.865 
[1] "0.3 - 115.9 (29.1)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  12Q LOSS MUTATED         0   101                0
  12Q LOSS WILD-TYPE       2   456                2
D64V3, multiclass
                  clus
vv                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  OMENTUM                         0                  2
  OVARY                         101                456
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, continuous
D64V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0 103
  12Q LOSS WILD-TYPE   3 465
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0  103
  12Q LOSS WILD-TYPE    3  465
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 0                  3
  YES              103                465
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  12Q LOSS MUTATED    2  4  0  1
  12Q LOSS WILD-TYPE 12 22  5  2
D64V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0                2                 12
  R1                4                 22
  R2                0                  5
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     3
  12Q LOSS WILD-TYPE                                3    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q LOSS MUTATED                           8
  12Q LOSS WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0    86
  12Q LOSS WILD-TYPE                                         1   389
D64V7, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                                8                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   86                389
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2  62
  12Q LOSS WILD-TYPE   8 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   62
  12Q LOSS WILD-TYPE    8  263
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               62                263
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   146 148
  13Q LOSS WILD-TYPE 120 142
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               294                262 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               148                142 
$`13Q LOSS MUTATED`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 
       41.00         1.81        18.51        11.87        63.09        21.57 
TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 
       32.52        76.57        71.47        56.55        41.59        38.37 
TCGA-04-1530 TCGA-04-1638 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 
      119.08        55.43        27.88        28.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 
       47.70        45.37        57.76        17.98         9.99        38.43 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       57.60        61.87        55.36        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-2044 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 
        8.55         6.12        71.11        63.09        20.94        26.93 
TCGA-10-0925 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0936 TCGA-10-0937 
       54.31        81.47        33.24        32.28        35.80        15.12 
TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0726 TCGA-13-0730 
       19.86        24.59        44.55         2.73        31.10        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 
       55.17         2.50        31.04        21.40         8.45        36.72 
TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 
       28.70        19.59         8.71         7.79         8.12         8.19 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0888 
       35.28        35.28        68.94       107.18        91.40        70.39 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       67.99        69.01        57.47        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0910 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       48.33        44.94        37.08        21.17        14.89        13.81 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1409 TCGA-13-1482 TCGA-13-1483 
        6.08        10.88         6.61         6.84        61.71        29.42 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       22.39        70.82        82.88        73.55        38.20        49.25 
TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       54.31        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1509 TCGA-13-1511 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FU 
        4.18         3.91        10.78         8.75         6.28         8.42 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1023 
       26.20        27.52        19.10        16.70        47.54        40.54 
TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 
       15.39        31.76        49.41         8.81        18.90         2.24 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 
       68.68         4.57        86.01       129.96         6.38        33.47 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       58.13         0.53       115.89        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 
        4.70         4.50        19.66        21.80         7.66        54.12 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1419 TCGA-24-1424 TCGA-24-1425 
       47.41         6.31         7.82         7.86         6.02         5.95 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 TCGA-24-1464 TCGA-24-1466 
        5.36        17.39        28.37        43.53        12.46        45.14 
TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 
        9.11        22.22        26.96        57.40        16.21        56.58 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 
       41.39        88.50        19.53        44.09        47.70        25.87 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       90.15        48.33        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1924 TCGA-24-1927 
        3.81         4.37        11.28         5.52        30.21        16.44 
TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       11.05         4.87       152.02        44.84        58.16        34.82 
TCGA-24-2030 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       53.95        57.07        36.16         0.79         0.36        47.54 
TCGA-24-2290 TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 
       36.23        26.96        51.06        34.98        65.00        33.96 
TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 
        2.96         0.36        20.61         0.30        60.59        35.54 
TCGA-25-1635 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       51.22        85.05        49.05         1.02        38.04         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 
       12.00        19.99        42.02         2.96        29.03        26.99 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
      101.79        38.53        31.20        68.32         0.53        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       18.67        59.67        41.98        66.81        62.93        39.12 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       31.23        22.55        12.36        11.84        12.30        14.93 
TCGA-29-1784 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-30-1860 TCGA-30-1861 
        5.36        62.47        42.25        11.84        44.91        34.78 
TCGA-30-1866 TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       36.62        30.05        18.77         6.71        42.51         2.20 
TCGA-36-1569 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1580 TCGA-36-1581 
       29.10        22.85        22.55         8.55        24.23        24.69 
TCGA-36-2529 TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2551 
       35.05        29.82        21.60         2.24        18.31        16.18 
TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2590 TCGA-57-1584 TCGA-57-1992 TCGA-59-2350 
        7.99        23.74         7.46        21.14        29.00        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 
      116.12         9.40        34.39        44.81        20.52         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       20.94        31.43        18.54         4.34        31.79        28.47 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1899 TCGA-61-1901 
       44.84        35.80         2.43        43.69         8.42        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 
       13.02         9.07        34.13        31.30        48.92        56.61 
TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-2002 TCGA-61-2012 
       67.76        15.75        38.17         2.01        17.98        30.64 
TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 
        1.18        45.40         4.80         4.77        71.74        60.62 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q 
       44.52       125.75        22.22         6.35        39.68        18.94 

$`13Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1346 TCGA-04-1348 
       40.24        49.15         2.01        46.62        65.52        48.76 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1371 
       63.98        65.46        49.28        44.32        33.67        82.39 
TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1649 TCGA-09-0364 
       19.99        29.10        84.20        48.89        64.64        29.16 
TCGA-09-0365 TCGA-09-0369 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1669 
        9.47        35.57        89.33        74.93        41.62        30.51 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 
       97.55         6.18        35.15         4.54       112.41        39.75 
TCGA-09-2056 TCGA-10-0926 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       12.46        25.91        18.51        11.70         3.91        35.44 
TCGA-13-0714 TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 TCGA-13-0757 TCGA-13-0758 
        6.21        39.58        12.39        15.19        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0791 TCGA-13-0794 TCGA-13-0801 
       11.54        34.06        32.25        38.93        30.35         8.28 
TCGA-13-0803 TCGA-13-0807 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0893 
       43.86        13.61        74.27        66.67        61.84        43.36 
TCGA-13-0899 TCGA-13-0905 TCGA-13-0908 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       56.15        47.84        44.84        27.72        34.06        29.98 
TCGA-13-0921 TCGA-13-0923 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 
        4.64         6.41         7.36         6.05         5.92         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 
        4.21         5.33        54.64        87.06        98.04        20.68 
TCGA-13-1491 TCGA-13-1496 TCGA-13-1498 TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 
       52.44         4.24        37.61         4.41         4.77         2.56 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FT TCGA-20-0987 
        3.09        14.24        12.23         8.61        54.77        23.05 
TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
       25.94        72.20        25.38         2.93         2.66        42.54 
TCGA-23-1026 TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       26.83        29.13        51.35        54.51         3.22        31.20 
TCGA-23-1117 TCGA-23-1120 TCGA-23-1122 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 
       33.30         4.27        39.09        24.95        87.48        91.66 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1416 
        7.63        11.64        41.56        22.32        63.55         6.38 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1427 TCGA-24-1431 TCGA-24-1434 
        7.99         0.76         6.25         4.83        19.17        18.67 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 
        8.55        72.92       105.99         3.45         1.18        64.27 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1562 
       41.06        51.91        58.09        70.62        39.88        45.50 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 
       10.26        17.23        88.37         5.79         9.80        22.68 
TCGA-24-1930 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       81.11       109.71        14.43        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       44.52        31.63        70.45        44.61         0.82        67.36 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 
       16.64        33.11        55.86        53.26         1.02        32.02 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 
       37.02         1.02        36.95         2.99        12.00        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1632 TCGA-25-1870 TCGA-25-1871 
       18.02        15.81         7.86        56.94        14.96        24.99 
TCGA-25-1877 TCGA-25-2042 TCGA-25-2398 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 
       18.05        13.02        45.01        31.00        78.90        44.71 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1696 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 
       47.18         0.79        33.70        18.25        29.23        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1781 
       17.00        85.68        22.98        24.36        17.33         8.38 
TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 
        7.23        34.62        86.17        65.00        45.11         4.90 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       11.47         9.76        21.04        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1867 
        2.47        15.68         0.26        48.10         6.12         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 
       57.57        24.26        48.79        45.57        30.18        22.49 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       44.12        28.77        21.53        30.08        25.74        27.85 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 
       33.01        29.49        25.91        25.08        23.80        20.98 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 
       20.52        14.17         6.05        11.47        26.04         9.44 
TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 
       42.02        40.77         1.48        24.03        11.38         1.74 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2355 
       22.32        25.08        25.02       180.20        80.12         2.14 
TCGA-59-2363 TCGA-61-1721 TCGA-61-1728 TCGA-61-1736 TCGA-61-1741 TCGA-61-1895 
        5.42        11.11        27.88        48.79        33.67         1.45 
TCGA-61-1900 TCGA-61-1910 TCGA-61-1911 TCGA-61-1917 TCGA-61-1998 TCGA-61-2000 
        5.79        37.05        42.51        43.43         5.52        14.50 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2017 TCGA-61-2092 TCGA-61-2095 
        4.01        30.64        39.85        45.96        51.72        61.64 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       58.39        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2613 TCGA-61-2614 TCGA-VG-A8LO TCGA-WR-A838 
       31.07         8.61         0.79         8.05 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.30               0.26 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            152.02             180.20 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            28.420             27.865 
[1] "0.3 - 152.0 (28.4)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  13Q LOSS MUTATED         1   295                2
  13Q LOSS WILD-TYPE       1   262                0
D65V3, multiclass
                  clus
vv                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         295                262
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V4, continuous
D65V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1 304
  13Q LOSS WILD-TYPE   2 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1  304
  13Q LOSS WILD-TYPE    2  264
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 1                  2
  YES              304                264
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED    4 10  2  2
  13Q LOSS WILD-TYPE 10 16  3  1
D65V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0                4                 10
  R1               10                 16
  R2                2                  3
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     9
  13Q LOSS WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q LOSS MUTATED                          21
  13Q LOSS WILD-TYPE                        11
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           1   251
  13Q LOSS WILD-TYPE                                         0   224
D65V7, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    9                  9
  BLACK OR AFRICAN AMERICAN                               21                 11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  251                224
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4 176
  13Q LOSS WILD-TYPE   6 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4  176
  13Q LOSS WILD-TYPE    6  149
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              176                149
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    91 115
  14Q LOSS WILD-TYPE 175 175
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               206                350 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               115                175 
$`14Q LOSS MUTATED`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1343 TCGA-04-1346 TCGA-04-1351 
       41.00         1.81         2.01        11.87        65.52        65.46 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1525 
       49.28        32.52        44.32        33.67        76.57        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1655 
      119.08        84.20        55.43        28.64        64.64        45.37 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       35.57         9.99        38.43        17.98         5.85         3.02 
TCGA-09-2048 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
        4.54        63.09        39.75        12.46        54.31        25.91 
TCGA-10-0928 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
       18.51        19.86        24.59        39.58         2.73        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       15.19        17.82        55.17        11.18        11.38        11.54 
TCGA-13-0761 TCGA-13-0766 TCGA-13-0792 TCGA-13-0794 TCGA-13-0803 TCGA-13-0884 
       34.06        21.40        36.72        30.35        43.86       107.18 
TCGA-13-0885 TCGA-13-0888 TCGA-13-0891 TCGA-13-0906 TCGA-13-0913 TCGA-13-0919 
       91.40        70.39        69.01        44.94        29.98        14.89 
TCGA-13-0920 TCGA-13-0921 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 TCGA-13-1481 
       13.81         4.64         7.36         6.05         4.21        87.06 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1496 TCGA-13-1497 
       22.39        70.82        82.88        52.44         4.24        54.31 
TCGA-13-1499 TCGA-13-1504 TCGA-13-1507 TCGA-13-1510 TCGA-13-2061 TCGA-13-2065 
       38.40        16.57         4.77         2.56        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FU TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1024 
        6.28         8.42        25.38        19.10         2.66        15.39 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 
       31.76        49.41        29.13        18.90        51.35        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 
        3.22        68.68        33.30        86.01       129.96        39.09 
TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2081 TCGA-23-2643 TCGA-24-0968 
       33.47        24.95       115.89        77.00         4.70        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1105 TCGA-24-1424 
       11.64        21.80        41.56        22.32        47.41         6.02 
TCGA-24-1427 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 
        4.83        18.67         8.55        72.92        45.14         9.11 
TCGA-24-1471 TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 
        1.18        26.96        64.27        16.21        56.58        51.91 
TCGA-24-1552 TCGA-24-1565 TCGA-24-1604 TCGA-24-1843 TCGA-24-1846 TCGA-24-1924 
       41.39        10.26        88.37         3.48         4.37        30.21 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 
        4.87       152.02        44.84        58.16        34.82        14.43 
TCGA-24-2260 TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 TCGA-24-2295 TCGA-25-1320 
       36.16        47.54        70.45         0.82        33.11        36.95 
TCGA-25-1323 TCGA-25-1626 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 
       12.00        15.81         0.30        56.94        35.54        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2391 TCGA-25-2393 TCGA-25-2400 
       14.96        24.99        18.05        49.05        38.04        42.02 
TCGA-25-2404 TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1707 
       29.03       101.79         0.79        31.20        68.32        41.98 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1771 
       29.23        17.00        66.81        39.12        22.98        22.55 
TCGA-29-1775 TCGA-29-1777 TCGA-29-2425 TCGA-29-2427 TCGA-29-2434 TCGA-29-A5NZ 
       12.36        12.30        65.00        62.47        11.47        21.04 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1859 TCGA-30-1861 TCGA-30-1887 TCGA-31-1944 
       51.91         2.47        48.10        34.78        24.26        45.57 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       18.77        22.49         6.71        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-2534 TCGA-36-2543 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 
       30.08        29.82         2.24        16.18        11.47        23.74 
TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       42.02        40.77         1.48        29.00        25.08        25.02 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1733 TCGA-61-1736 TCGA-61-1740 
       44.81        20.52         8.09        31.79        48.79         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1917 
       33.67        43.69        11.41         9.07        34.13        43.43 
TCGA-61-2000 TCGA-61-2009 TCGA-61-2088 TCGA-61-2102 TCGA-61-2109 TCGA-61-2614 
       14.50        39.85         4.77         6.48        20.68         8.61 
TCGA-OY-A56P TCGA-OY-A56Q 
       39.68        18.94 

$`14Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 
       40.24        49.15        46.62        18.51        63.09        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       21.57        63.98        71.47        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1536 TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 
       19.99        29.10        48.89        27.88        36.23        31.86 
TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1662 
       47.70        29.16         9.47        57.76        17.98        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       74.93        41.62        57.60        61.87        55.36        30.51 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 
        8.55        97.55         6.18         6.12        35.15       112.41 
TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 
       71.11        20.94        26.93        81.47        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 
       11.70         3.91        35.44        35.80        15.12         6.21 
TCGA-13-0720 TCGA-13-0725 TCGA-13-0755 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 
       44.55        12.39         2.50        32.25        31.04         8.45 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       38.93        28.70        19.59         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.28         8.19        35.28        35.28        13.61        68.94 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 
       74.27        66.67        61.84        67.99        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       56.15        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0923 
       44.84        37.08        27.72        34.06        21.17         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.08        10.88         6.61         5.92         6.84         4.70 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
        5.33        54.64        61.71        29.42        98.04        20.68 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
       73.55        38.20        49.25        37.61        13.97        32.84 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
        4.21         4.41         4.18         3.91         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       12.23         8.61        54.77        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 
       72.20        27.52        16.70         2.93        47.54        42.54 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1029 TCGA-23-1032 TCGA-23-1113 TCGA-23-1116 
       40.54        26.83         8.81         2.24        31.20         4.57 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 
        4.27         6.38        58.13         0.53        87.48        91.66 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0966 TCGA-24-0980 TCGA-24-1103 
       49.84         2.76         4.50         7.63         7.66        54.12 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       63.55         6.31         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 
        0.76         6.25         5.95         5.36        17.39        28.37 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 
       19.17        43.53        12.46       105.99         3.45        22.22 
TCGA-24-1545 TCGA-24-1550 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       57.40        41.06        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 
       19.53        44.09        45.50        47.70        25.87        17.23 
TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 
       90.15        48.33        38.24         8.32         3.72         3.81 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 
       11.28         5.79         5.52         9.80        22.68        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       11.05        81.11       109.71        53.95        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 
       64.01        44.52        57.07         0.79         0.36        31.63 
TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 
       44.61        67.36        36.23        16.64        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        32.02        51.06        37.02         1.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
       34.98        65.00        33.96         2.99         2.96        18.58 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1633 TCGA-25-1878 
       18.02         0.36        20.61         7.86        60.59        85.05 
TCGA-25-2042 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       13.02         1.02         3.02        12.00        45.01        19.99 
TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 
        2.96        31.00        26.99        78.90        44.71        47.18 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       38.53        33.70         0.53        16.90        18.67        59.67 
TCGA-29-1705 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 
       18.25        34.62        85.68        62.93        31.23        24.36 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       17.33        11.84        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       34.62        86.17        45.11         4.90        42.25        11.84 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 
        9.76        38.07        36.26        15.68         0.26        44.91 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
        6.12        36.62         1.22        57.57        30.05        48.79 
TCGA-31-1946 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       30.18        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
       21.53        25.74        27.85        24.23        24.69        35.05 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       33.01        29.49        25.91        25.08        23.80        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-3P-A9WA 
       20.98        18.31        20.52        14.17         6.05         7.99 
TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       26.04         9.44         7.46        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
        1.74        22.32       180.20        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 
        9.40        34.39         2.14         5.42        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1737 
       31.43        18.54        27.88         4.34        28.47        44.84 
TCGA-61-1738 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 
       35.80         1.45         8.42         5.79        13.02        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 
       37.05        42.51        48.92        56.61        67.76        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
       38.17         2.01         5.52        17.98         4.01        30.64 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
       30.64         1.18        45.96        45.40         4.80        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       76.87        44.52       125.75        22.22         6.35        31.07 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.30               0.26 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            152.02             180.20 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            29.015             27.865 
[1] "0.3 - 152.0 (29.0)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  14Q LOSS MUTATED         0   207                1
  14Q LOSS WILD-TYPE       2   350                1
D66V3, multiclass
                  clus
vv                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  OMENTUM                         0                  2
  OVARY                         207                350
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V4, continuous
D66V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     0 212
  14Q LOSS WILD-TYPE   3 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      0  212
  14Q LOSS WILD-TYPE    3  356
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 0                  3
  YES              212                356
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS MUTATED    5  7  3  1
  14Q LOSS WILD-TYPE  9 19  2  2
D66V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0                5                  9
  R1                7                 19
  R2                3                  2
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  2     4
  14Q LOSS WILD-TYPE                                1    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q LOSS MUTATED                          11
  14Q LOSS WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           0   181
  14Q LOSS WILD-TYPE                                         1   294
D66V7, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  1
  ASIAN                                                    4                 14
  BLACK OR AFRICAN AMERICAN                               11                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  181                294
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     6 120
  14Q LOSS WILD-TYPE   4 205
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      6  120
  14Q LOSS WILD-TYPE    4  205
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  4
  NOT HISPANIC OR LATINO              120                205
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   116 152
  15Q LOSS WILD-TYPE 150 138
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               268                288 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               152                138 
$`15Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1338 TCGA-04-1342 TCGA-04-1347 TCGA-04-1350 TCGA-04-1356 
       40.24        46.62        18.51        63.09        63.98        49.28 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 
       71.47        82.39        56.55        19.99        38.37        29.10 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       27.88        28.64        64.64        31.86        45.37        29.16 
TCGA-09-0365 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
        9.47         9.99        38.43        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1674 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-10-0925 
       17.98         8.55        71.11        63.09        20.94        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 
       25.91        81.47        35.80        24.59        39.58         2.73 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 
       17.82        55.17        11.18        11.38        11.54        32.25 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0802 TCGA-13-0803 TCGA-13-0807 TCGA-13-0883 
       28.70        30.35         8.19        43.86        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 
      107.18        91.40        66.67        70.39        61.84        69.01 
TCGA-13-0899 TCGA-13-0910 TCGA-13-0911 TCGA-13-0921 TCGA-13-0923 TCGA-13-1405 
       56.15        37.08        27.72         4.64         6.41         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1482 
        6.05         5.92         6.84         4.70         4.21        61.71 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 
       98.04        22.39        70.82        82.88        52.44        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       49.25         4.24        16.57         4.21         4.41         4.77 
TCGA-13-1510 TCGA-13-2057 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
        2.56        14.24        10.78         8.42        25.94        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-23-1022 TCGA-23-1030 
       27.52        25.38        19.10         2.93        42.54        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
       18.90         2.24        51.35        54.51        31.20        68.68 
TCGA-23-1116 TCGA-23-1123 TCGA-23-2077 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
        4.57        33.47       115.89        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0968 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 
        4.50        19.66        41.56        22.32        63.55        47.41 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 
        7.82         7.99         0.76         6.02         5.36        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 
       28.37        19.17        18.67         8.55        72.92        45.14 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
        9.11         1.18        26.96        16.21        56.58        41.06 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1564 TCGA-24-1603 
       41.39        58.09        70.62        39.88        25.87        90.15 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       48.33        38.24         8.32         3.48         3.72         3.81 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 
        5.52         9.80        30.21        16.44        11.05         4.87 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 
      152.02        34.82        53.95        64.01        57.07        36.16 
TCGA-24-2261 TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
        0.79        70.45         0.82        16.64        33.11        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 TCGA-25-1318 
       53.26         1.02        26.96        32.02        37.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       65.00        36.95        33.96         2.99        12.00         2.96 
TCGA-25-1623 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       18.58        20.61         0.30        56.94        60.59        35.54 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2396 TCGA-25-2397 TCGA-25-2404 TCGA-29-1693 
       24.99        18.05         3.02        12.00        29.03       101.79 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 
        0.79        68.32         0.53        18.67        59.67        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       29.23        34.62        17.00        85.68        66.81        62.93 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1777 TCGA-29-1783 
       39.12        22.98        24.36        17.33        12.30         7.23 
TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 
        5.36        86.17        65.00        45.11         4.90        11.84 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
       11.47        38.07        51.91         2.47        15.68        48.10 
TCGA-30-1860 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 
       44.91        36.62         1.22        24.26        30.05        48.79 
TCGA-31-1950 TCGA-31-1953 TCGA-36-1581 TCGA-36-2529 TCGA-36-2543 TCGA-36-2545 
       18.77         6.71        24.69        35.05         2.24        18.31 
TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 TCGA-42-2593 TCGA-57-1583 
       14.17        16.18        11.47        42.02         1.48        11.38 
TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-61-1724 
       22.32        25.08       180.20        22.32       116.12        20.94 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 
       18.54        27.88        31.79        28.47        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 
        2.43        33.67        43.69        11.41         9.07        34.13 
TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 
       56.61        43.43        15.75        38.17         4.01        30.64 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2092 TCGA-61-2094 TCGA-61-2096 TCGA-61-2098 
       30.64         1.18        51.72        71.74        58.39        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        76.87        44.52       125.75        22.22 
TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
        6.35         8.61        39.68        18.94 

$`15Q LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1343 TCGA-04-1346 
       41.00         1.81        49.15         2.01        11.87        65.52 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       48.76        21.57        65.46        32.52        44.32        33.67 
TCGA-04-1365 TCGA-04-1516 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       76.57        41.59       119.08        84.20        55.43        48.89 
TCGA-04-1651 TCGA-04-1654 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1662 
       36.23        47.70        57.76        17.98        35.57        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 
       74.93        41.62        57.60         5.85         3.02        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2053 
        6.18         6.12        35.15         4.54       112.41        39.75 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       26.93        12.46        18.51        33.24        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 
        3.91        35.44        15.12        19.86         6.21        44.55 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0761 TCGA-13-0764 
       12.39        31.10        15.19         2.50        34.06        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 TCGA-13-0797 
       21.40         8.45        38.93        36.72        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 TCGA-13-0886 
        7.79         8.12         8.28        35.28        35.28        74.27 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       67.99        43.36        57.47        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 
       48.33        47.84        44.94        44.84        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       21.17        14.89        13.81         6.08        10.88         6.61 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1492 
        5.33        54.64        87.06        29.42        20.68        73.55 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1509 
       54.31        37.61        38.40        13.97        32.84         4.18 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 
        3.91         3.09        12.23         8.61         8.75         6.28 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 
       54.77        23.05        72.20        16.70         2.66        47.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        31.76        49.41         8.81 
TCGA-23-1111 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
        3.22        33.30        86.01       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 
       39.09        58.13         0.53        24.95        87.48        91.66 
TCGA-23-2081 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 
       77.00         7.63        11.64        21.80         7.66        54.12 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 
        6.31         6.38         7.86         6.25         5.95         4.83 
TCGA-24-1435 TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1545 
       43.53        12.46       105.99         3.45        22.22        57.40 
TCGA-24-1546 TCGA-24-1551 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       64.27        51.91        88.50        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1846 TCGA-24-1847 
       47.70        10.26        17.23        88.37         4.37        11.28 
TCGA-24-1849 TCGA-24-1923 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 
        5.79        22.68        81.11        44.84        58.16       109.71 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 TCGA-24-2262 TCGA-24-2267 
       14.43        18.48        28.18        44.52         0.36        47.54 
TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-25-1315 TCGA-25-1317 
       31.63        44.61        67.36        36.23        51.06         1.02 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1635 TCGA-25-1870 
       18.02        15.81         0.36         7.86        51.22        14.96 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 
       85.05        13.02        49.05         1.02        38.04        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       19.99        42.02         2.96        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 
       44.71        47.18        38.53        33.70        31.20        16.90 
TCGA-29-1705 TCGA-29-1768 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 
       18.25        31.23        22.55        12.36        11.84        14.93 
TCGA-29-1781 TCGA-29-1785 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ 
        8.38        34.62        62.47        42.25         9.76        21.04 
TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1880 TCGA-31-1944 
       36.26         0.26        34.78         6.12        57.57        45.57 
TCGA-31-1946 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       30.18        22.49        42.51        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       25.74        27.85        24.23        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 
       25.91        25.08        23.80        21.60        20.98        20.52 
TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 
        6.05         7.99        26.04        23.74         9.44         7.46 
TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1994 
       40.77        24.03        21.14         1.74        29.00        25.02 
TCGA-59-2349 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 
       80.12         9.40        34.39         2.14         5.42        44.81 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 TCGA-61-1736 
       20.52        11.11         8.09        31.43         4.34        48.79 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 
        1.45         8.42         5.79        13.02        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       42.51        48.92        67.76         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       17.98        39.85        45.96        45.40         4.80         4.77 
TCGA-61-2095 TCGA-61-2097 TCGA-61-2109 TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 
       61.64        60.62        20.68        31.07         0.79         8.05 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.30               0.26 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            180.20             129.96 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            28.555             26.960 
[1] "0.3 - 180.2 (28.6)" "0.3 - 130.0 (27.0)"
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  15Q LOSS MUTATED         1   268                2
  15Q LOSS WILD-TYPE       1   289                0
D67V3, multiclass
                  clus
vv                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         268                289
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V4, continuous
D67V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2 274
  15Q LOSS WILD-TYPE   1 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2  274
  15Q LOSS WILD-TYPE    1  294
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 2                  1
  YES              274                294
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED    5 13  3  1
  15Q LOSS WILD-TYPE  9 13  2  2
D67V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0                5                  9
  R1               13                 13
  R2                3                  2
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  2     6
  15Q LOSS WILD-TYPE                                1    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q LOSS MUTATED                          15
  15Q LOSS WILD-TYPE                        17
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           0   236
  15Q LOSS WILD-TYPE                                         1   239
D67V7, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  1
  ASIAN                                                    6                 12
  BLACK OR AFRICAN AMERICAN                               15                 17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  236                239
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     6 151
  15Q LOSS WILD-TYPE   4 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6  151
  15Q LOSS WILD-TYPE    4  174
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  4
  NOT HISPANIC OR LATINO              151                174
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED   150 171
  16P LOSS WILD-TYPE 116 119
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               321                235 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               171                119 
$`16P LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1347 
       40.24        41.00         2.01        46.62        11.87        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 
       21.57        63.98        49.28        44.32        33.67        71.47 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 
       41.59        19.99       119.08        55.43        48.89        64.64 
TCGA-04-1652 TCGA-09-0367 TCGA-09-1659 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       31.86        17.98         9.99        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 
       55.36        30.51        17.98         3.02        97.55         6.18 
TCGA-09-2044 TCGA-09-2049 TCGA-09-2053 TCGA-09-2054 TCGA-10-0925 TCGA-10-0926 
        6.12       112.41        39.75        20.94        54.31        25.91 
TCGA-10-0928 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       18.51        35.44        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
       44.55        39.58        15.19        17.82        55.17        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.38        11.54        34.06        32.25        31.04        21.40 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0801 TCGA-13-0805 
       38.93        28.70        30.35        19.59         8.28        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0903 TCGA-13-0904 
       70.39        69.01        43.36        56.15        47.38        48.33 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 
       44.94        37.08        27.72        34.06        21.17        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1484 
        6.05         5.92         4.70         4.21        87.06        98.04 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1505 TCGA-13-1506 
        4.24        54.31        38.40        13.97         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 
        4.77         4.18         3.91         3.09        14.24        10.78 
TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 TCGA-20-1683 TCGA-20-1687 TCGA-23-1022 
        8.75        54.77        25.94        25.38         2.66        42.54 
TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       15.39        31.76        49.41        29.13        18.90         2.24 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       51.35         3.22        31.20        68.68         4.57        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       86.01       129.96         4.27         6.38        39.09        33.47 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
       24.95        87.48         4.50        11.64        21.80        41.56 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 
       63.55        47.41         6.38         7.82         7.99         7.86 
TCGA-24-1422 TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 TCGA-24-1463 
        0.76         5.36        17.39        19.17         8.55        72.92 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1548 
       45.14         9.11         1.18        22.22        57.40        16.21 
TCGA-24-1552 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       41.39        88.50        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 
       25.87        17.23        90.15         3.48         3.72         4.37 
TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 
       11.28         5.52        22.68        30.21        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
        4.87       152.02        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 
       14.43        28.18        64.01        36.16         0.36        47.54 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 
       70.45        44.61         0.82        36.23        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26        26.96        32.02        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
        1.02        34.98        65.00        36.95         2.99        12.00 
TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
        2.96        15.81         0.36        20.61         0.30        56.94 
TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       60.59        51.22        14.96        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 
       38.04         3.02        12.00        45.01        42.02         2.96 
TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1697 TCGA-29-1699 
       29.03        26.99        78.90       101.79        31.20         0.53 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 
       16.90        59.67        18.25        17.00        85.68        62.93 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 
       39.12        22.98        24.36        22.55        12.36        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 
        8.38         7.23        34.62        65.00        45.11        42.25 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       38.07        51.91        36.26         2.47        15.68         0.26 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-31-1944 
       44.91        34.78        36.62         1.22        24.26        45.57 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 
       18.77        22.49         6.71        42.51         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       29.10        21.53        22.85         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-2532 TCGA-36-2534 TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 
       27.85        29.49        29.82         2.24        14.17        16.18 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1992 
       42.02         7.46         1.48        24.03        21.14        29.00 
TCGA-57-1993 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 
       25.08        22.32       116.12         9.40         2.14         5.42 
TCGA-59-A5PD TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 TCGA-61-1736 TCGA-61-1737 
       20.52         8.09        31.43         4.34        48.79        44.84 
TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
       33.67         1.45         8.42         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1914 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2003 
       37.05        56.61        38.17         2.01         5.52         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 
       30.64        30.64         4.77        71.74        60.62        65.52 
TCGA-61-2102 TCGA-61-2109 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
        6.48        20.68        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
       39.68         0.79         8.05 

$`16P LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1342 TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 
        1.81        49.15        18.51        65.52        48.76        65.46 
TCGA-04-1361 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 TCGA-04-1525 TCGA-04-1536 
       32.52        76.57        82.39        56.55        38.37        29.10 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 
       84.20        27.88        28.64        36.23        47.70        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 
       29.16         9.47        57.76        35.57        38.43        89.33 
TCGA-09-1664 TCGA-09-1672 TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
       74.93         5.85         8.55        35.15         4.54        71.11 
TCGA-09-2051 TCGA-09-2055 TCGA-09-2056 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 
       63.09        26.93        12.46        81.47        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       11.70         3.91        35.80         2.73        12.39        31.10 
TCGA-13-0755 TCGA-13-0768 TCGA-13-0792 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
        2.50         8.45        36.72         8.71         7.79         8.12 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0889 TCGA-13-0890 TCGA-13-0897 
        8.19        43.86        35.28        61.84        67.99        57.47 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0905 TCGA-13-0908 TCGA-13-0913 TCGA-13-0921 
       57.07        19.36        47.84        44.84        29.98         4.64 
TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 
        6.84         5.33        54.64        61.71        29.42        20.68 
TCGA-13-1487 TCGA-13-1498 TCGA-13-1501 TCGA-13-1504 TCGA-13-1510 TCGA-13-2059 
       22.39        37.61        32.84        16.57         2.56        12.23 
TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 
        8.61         6.28         8.42        23.05        26.20        72.20 
TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1023 
       27.52        19.10        16.70         2.93        47.54        40.54 
TCGA-23-1026 TCGA-23-1029 TCGA-23-1110 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
       26.83         8.81        54.51        58.13         0.53       115.89 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 
       91.66        77.00        49.84         2.76         4.70         7.63 
TCGA-24-0968 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1413 TCGA-24-1423 
       19.66         7.66        22.32        54.12         6.31         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        6.02         5.95         4.83        28.37        18.67        43.53 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1544 TCGA-24-1546 TCGA-24-1549 
       12.46       105.99         3.45        26.96        64.27        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1565 
       41.06        51.91        58.09        70.62        39.88        10.26 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-24-1849 
       88.37        48.33        38.24         8.32         3.81         5.79 
TCGA-24-1920 TCGA-24-1927 TCGA-24-2030 TCGA-24-2033 TCGA-24-2038 TCGA-24-2254 
        9.80        16.44        53.95        18.48        44.52        57.07 
TCGA-24-2261 TCGA-24-2271 TCGA-24-2289 TCGA-25-1312 TCGA-25-1321 TCGA-25-1623 
        0.79        31.63        67.36         1.02        33.96        18.58 
TCGA-25-1625 TCGA-25-1630 TCGA-25-1634 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       18.02         7.86        35.54        24.99        18.05        85.05 
TCGA-25-2399 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 
       19.99        31.00        44.71        47.18        38.53         0.79 
TCGA-29-1696 TCGA-29-1698 TCGA-29-1702 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       33.70        68.32        18.67        41.98        29.23        34.62 
TCGA-29-1763 TCGA-29-1768 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1784 
       66.81        31.23        17.33        11.84        14.93         5.36 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       86.17        62.47         4.90        11.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1859 TCGA-30-1862 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
       21.04        48.10         6.12        57.57        30.05        48.79 
TCGA-31-1946 TCGA-31-1956 TCGA-36-1574 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
       30.18        44.12        22.55        24.23        24.69        35.05 
TCGA-36-2530 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 
       33.01        25.91        25.08        23.80        21.60        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 
       18.31        20.52         6.05        11.47         7.99        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 
       23.74         9.44        40.77        11.38         1.74        22.32 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2354 TCGA-59-2372 TCGA-61-1721 
       25.02       180.20        80.12        34.39        44.81        11.11 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1738 
       20.94        18.54        27.88        31.79        28.47        35.80 
TCGA-61-1740 TCGA-61-1743 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1911 
        2.43        43.69         5.79        11.41        13.02        42.51 
TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 TCGA-61-2002 
       48.92        67.76        43.43        15.75        14.50        17.98 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 
       39.85         1.18        45.96        45.40         4.80        51.72 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 
       61.64        58.39        55.50        76.87        44.52       125.75 
TCGA-OY-A56Q 
       18.94 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.26               0.53 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            152.02             180.20 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             27.72              28.47 
[1] "0.3 - 152.0 (27.7)" "0.5 - 180.2 (28.5)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  16P LOSS MUTATED         2   320                1
  16P LOSS WILD-TYPE       0   237                1
D68V3, multiclass
                  clus
vv                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  OMENTUM                         2                  0
  OVARY                         320                237
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V4, continuous
D68V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3 327
  16P LOSS WILD-TYPE   0 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3  327
  16P LOSS WILD-TYPE    0  241
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 3                  0
  YES              327                241
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  16P LOSS MUTATED    6 13  3  1
  16P LOSS WILD-TYPE  8 13  2  2
D68V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                6                  8
  R1               13                 13
  R2                3                  2
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  3    10
  16P LOSS WILD-TYPE                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P LOSS MUTATED                          16
  16P LOSS WILD-TYPE                        16
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           1   278
  16P LOSS WILD-TYPE                                         0   197
D68V7, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                   10                  8
  BLACK OR AFRICAN AMERICAN                               16                 16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  278                197
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3 195
  16P LOSS WILD-TYPE   7 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3  195
  16P LOSS WILD-TYPE    7  130
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  7
  NOT HISPANIC OR LATINO              195                130
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   184 213
  16Q LOSS WILD-TYPE  82  77
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               397                159 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               213                 77 
$`16Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       11.87        65.52        63.09        21.57        63.98        49.28 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 
       44.32        33.67        76.57        71.47        82.39        41.59 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1649 
       19.99        38.37       119.08        55.43        48.89        64.64 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 
       31.86        47.70        45.37        57.76        17.98         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       38.43        89.33        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       30.51        17.98         8.55        97.55         6.18         6.12 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-10-0925 
        4.54       112.41        63.09        39.75        20.94        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0935 TCGA-10-0936 
       25.91        81.47        18.51        32.28        35.44        35.80 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       15.12        19.86         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
        2.73        31.10        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       11.18        11.38        11.54        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       21.40        38.93        28.70        30.35        19.59         8.71 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.28         8.19        35.28        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
      107.18        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0903 TCGA-13-0906 TCGA-13-0908 
       69.01        43.36        56.15        47.38        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       37.08        27.72        34.06        21.17        14.89        13.81 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        6.41         6.08        10.88         6.61         7.36         6.05 
TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 
        5.92         4.70         4.21        87.06        29.42        98.04 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       49.25         4.24        54.31        37.61        38.40        13.97 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 
        4.21         4.41         4.77         4.18         3.91         3.09 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       14.24         8.61        10.78         8.75        54.77         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 
       23.05        25.94        26.20        27.52        25.38        16.70 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 
        2.93         2.66        42.54        40.54        15.39        31.76 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       49.41         8.81        29.13        18.90         2.24        51.35 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
        3.22        31.20        68.68         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 
      129.96         4.27         6.38        39.09        33.47        24.95 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       87.48        77.00         2.76         4.70         4.50         7.63 
TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
       11.64        41.56        22.32        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1425 
        6.38         7.82         7.99         7.86         0.76         5.95 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.36        17.39        28.37        19.17        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 
        8.55        72.92        45.14         9.11         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       26.96        57.40        16.21        41.06        51.91        41.39 
TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       88.50        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       10.26        17.23        90.15         8.32         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        4.37        11.28         5.52        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       11.05        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2260 
       34.82        14.43        53.95        28.18        64.01        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
        0.82        16.64        33.11        55.86        53.26         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        32.02        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 
       65.00        36.95         2.99        12.00         2.96        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 
        0.36        20.61         0.30        56.94        60.59        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       14.96        24.99        18.05        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
        1.02        38.04         3.02        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1691 TCGA-29-1693 
       42.02         2.96        29.03        26.99        47.18       101.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       33.70        31.20        68.32         0.53        16.90        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 
       59.67        18.25        17.00        85.68        62.93        39.12 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 
       31.23        22.98        24.36        22.55        12.36        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
        8.38         7.23         5.36        34.62        86.17        65.00 
TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       45.11        42.25        11.84        21.04        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 
       36.26         2.47        15.68         0.26        44.91        34.78 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 
       36.62         1.22        24.26        48.79        45.57        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
       22.49         6.71         2.20        28.77        29.10        21.53 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.85         8.55        30.08        25.74        27.85        24.23 
TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 TCGA-36-2548 
       35.05        29.49        29.82        21.60         2.24        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 
       16.18        11.47        42.02         7.46         1.48        24.03 
TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 TCGA-59-2352 
       21.14        29.00        25.08        25.02        22.32         9.40 
TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 
        2.14         5.42        20.52         8.09        31.43        18.54 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 
        4.34        31.79        48.79        44.84        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        1.45         8.42         5.79         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       37.05        48.92        56.61        38.17         2.01         5.52 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 
        4.01        30.64        30.64         4.80         4.77        71.74 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 
       60.62        65.52         6.48        76.87        20.68       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO 
       22.22         6.35        31.07         8.61        39.68         0.79 
TCGA-WR-A838 
        8.05 

$`16Q LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1348 TCGA-04-1351 TCGA-04-1361 TCGA-04-1514 TCGA-04-1536 
        1.81        48.76        65.46        32.52        56.55        29.10 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-09-0364 TCGA-09-0365 
       84.20        27.88        28.64        36.23        29.16         9.47 
TCGA-09-0369 TCGA-09-1664 TCGA-09-1672 TCGA-09-1673 TCGA-09-2045 TCGA-09-2050 
       35.57        74.93         5.85         3.02        35.15        71.11 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 TCGA-13-0725 
       26.93        12.46        33.24        11.70         3.91        12.39 
TCGA-13-0768 TCGA-13-0792 TCGA-13-0799 TCGA-13-0800 TCGA-13-0803 TCGA-13-0890 
        8.45        36.72         7.79         8.12        43.86        67.99 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0913 
       57.47        57.07        19.36        48.33        47.84        29.98 
TCGA-13-0921 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 
        4.64         6.84         5.33        54.64        61.71        20.68 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1510 TCGA-13-2059 TCGA-13-2071 TCGA-20-0996 
       32.84        16.57         2.56        12.23         6.28        72.20 
TCGA-20-1684 TCGA-23-1021 TCGA-23-1026 TCGA-23-1110 TCGA-23-1124 TCGA-23-1809 
       19.10        47.54        26.83        54.51        58.13         0.53 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2084 TCGA-24-0968 TCGA-24-0975 TCGA-24-0980 
      115.89        91.66        49.84        19.66        21.80         7.66 
TCGA-24-1103 TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1464 TCGA-24-1467 
       54.12         6.25         6.02         4.83        12.46       105.99 
TCGA-24-1470 TCGA-24-1546 TCGA-24-1549 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 
        3.45        64.27        56.58        58.09        70.62        39.88 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1845 TCGA-24-1849 TCGA-24-1920 
       88.37        48.33        38.24         3.81         5.79         9.80 
TCGA-24-2027 TCGA-24-2033 TCGA-24-2038 TCGA-24-2254 TCGA-24-2289 TCGA-24-2290 
      109.71        18.48        44.52        57.07        67.36        36.23 
TCGA-25-1321 TCGA-25-1623 TCGA-25-1625 TCGA-25-1630 TCGA-25-1634 TCGA-25-2408 
       33.96        18.58        18.02         7.86        35.54        31.00 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 TCGA-29-1707 TCGA-29-1710 
       78.90        44.71        38.53         0.79        41.98        29.23 
TCGA-29-1711 TCGA-29-1763 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-2427 
       34.62        66.81        17.33        11.84        14.93        62.47 
TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-30-1859 TCGA-30-1862 TCGA-30-1880 
        4.90        11.47         9.76        48.10         6.12        57.57 
TCGA-30-1891 TCGA-31-1946 TCGA-31-1955 TCGA-31-1956 TCGA-36-1574 TCGA-36-1581 
       30.05        30.18        42.51        44.12        22.55        24.69 
TCGA-36-2530 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2545 
       33.01        25.91        25.08        23.80        20.98        18.31 
TCGA-36-2547 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       20.52         6.05         7.99        26.04        23.74         9.44 
TCGA-42-2591 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 
       40.77        11.38         1.74        22.32       180.20        80.12 
TCGA-59-2351 TCGA-59-2354 TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1728 
      116.12        34.39        44.81        11.11        20.94        27.88 
TCGA-61-1734 TCGA-61-1738 TCGA-61-1740 TCGA-61-1901 TCGA-61-1903 TCGA-61-1911 
       28.47        35.80         2.43        11.41        13.02        42.51 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 
       67.76        43.43        15.75        14.50        17.98        39.85 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 
        1.18        45.96        45.40        51.72        61.64        58.39 
TCGA-61-2101 TCGA-61-2110 TCGA-OY-A56Q 
       55.50        44.52        18.94 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.26               0.53 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            152.02             180.20 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             26.96              29.23 
[1] "0.3 - 152.0 (27.0)" "0.5 - 180.2 (29.2)"
[1] "hr=" "1.2"
D69V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  16Q LOSS MUTATED         1   396                2
  16Q LOSS WILD-TYPE       1   161                0
D69V3, multiclass
                  clus
vv                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         396                161
  PERITONEUM OVARY                2                  0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V4, continuous
D69V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3 405
  16Q LOSS WILD-TYPE   0 163
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3  405
  16Q LOSS WILD-TYPE    0  163
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 3                  0
  YES              405                163
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  16Q LOSS MUTATED    7 17  4  1
  16Q LOSS WILD-TYPE  7  9  1  2
D69V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0                7                  7
  R1               17                  9
  R2                4                  1
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  3    13
  16Q LOSS WILD-TYPE                                0     5
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q LOSS MUTATED                          22
  16Q LOSS WILD-TYPE                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           1   340
  16Q LOSS WILD-TYPE                                         0   135
D69V7, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                   13                  5
  BLACK OR AFRICAN AMERICAN                               22                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  340                135
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     5 234
  16Q LOSS WILD-TYPE   5  91
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5  234
  16Q LOSS WILD-TYPE    5   91
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  5
  NOT HISPANIC OR LATINO              234                 91
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   216 245
  17P LOSS WILD-TYPE  50  45
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               461                 95 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               245                 45 
$`17P LOSS MUTATED`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 TCGA-04-1347 
       40.24         1.81        49.15        46.62        11.87        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 
       48.76        21.57        63.98        65.46        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       33.67        76.57        71.47        82.39        56.55        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       38.37       119.08        29.10        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 
       45.37        29.16         9.47        57.76        17.98         9.99 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       89.33        74.93        57.60        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
       17.98         5.85         3.02        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-10-0926 
      112.41        71.11        39.75        20.94        26.93        25.91 
TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       81.47        33.24        11.70        35.80        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
        6.21        24.59        44.55        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       31.10        15.19        17.82         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       11.54        34.06        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       28.70        30.35        19.59         8.71         7.79         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.19        43.86        35.28        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
      107.18        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       67.99        69.01        43.36        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       48.33        47.84        44.84        37.08        27.72        34.06 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        14.89         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.61         7.36         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 
        4.21        87.06        61.71        29.42        98.04        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       54.31        37.61        38.40        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2061 
        4.21         4.41         4.18         2.56         3.91        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.75         6.28        54.77         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       26.20        27.52        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        40.54        15.39        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        8.81        29.13        18.90         2.24        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
        3.22        31.20         4.57        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
        4.27         6.38        39.09        33.47        58.13        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
      115.89        87.48        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        11.64        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
        7.66        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.38         7.82         7.99         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        5.95         5.36         4.83        17.39        28.37        19.17 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       18.67        43.53         8.55        72.92        12.46        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 
      105.99         9.11         3.45         1.18        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       64.27        16.21        56.58        41.06        51.91        41.39 
TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       88.50        39.88        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       25.87        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        8.32         3.48         3.72         4.37        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        5.52         9.80        22.68        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
        4.87       152.02        44.84        58.16        34.82       109.71 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2261 TCGA-24-2267 
       14.43        53.95        18.48        64.01         0.79        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 
       31.63        70.45        44.61         0.82        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       33.11        55.86        53.26         1.02        26.96        32.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       51.06        37.02         1.02        34.98        65.00        36.95 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1627 
       33.96         2.99        12.00         2.96        18.02         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       20.61         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 
       51.22        14.96        24.99        18.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
        1.02        38.04         3.02        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 
        2.96        29.03        26.99        78.90        47.18       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       38.53         0.79        33.70        31.20        68.32         0.53 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 
       16.90        59.67        18.25        41.98        34.62        17.00 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       85.68        62.93        31.23        22.98        24.36        22.55 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       12.36        11.84        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        5.36        34.62        86.17        65.00        62.47        45.11 
TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       42.25        11.84        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 
       15.68         0.26        48.10        44.91        34.78        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        1.22        57.57        24.26        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 
       30.18        18.77        22.49         6.71        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
        2.20        28.77        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       30.08        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       25.08         2.24        20.98        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 
        6.05        16.18         7.99        26.04        23.74        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
        7.46        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 
        1.74        25.08       180.20        22.32       116.12        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1725 
        2.14         5.42        44.81        20.52        20.94        31.43 
TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       18.54        27.88         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       44.84        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
        8.42        11.41        13.02        34.13        31.30        37.05 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
       48.92        56.61        67.76        43.43        15.75        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
        2.01         5.52        14.50        17.98         4.01        30.64 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2095 
       30.64         1.18         4.80         4.77        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       58.39        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       20.68        44.52       125.75        22.22         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        8.61        39.68        18.94         0.79         8.05 

$`17P LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1337 TCGA-04-1342 TCGA-04-1346 TCGA-04-1356 TCGA-04-1516 
       41.00         2.01        18.51        65.52        49.28        41.59 
TCGA-09-0369 TCGA-09-1661 TCGA-09-1665 TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 
       35.57        38.43        41.62         8.55         6.18         4.54 
TCGA-09-2051 TCGA-09-2056 TCGA-10-0925 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 
       63.09        12.46        54.31        18.51        32.28         3.91 
TCGA-10-0935 TCGA-13-0751 TCGA-13-0762 TCGA-13-0764 TCGA-13-0800 TCGA-13-0897 
       35.44        55.17        32.25        31.04         8.12        57.47 
TCGA-13-0899 TCGA-13-0906 TCGA-13-0913 TCGA-13-0920 TCGA-13-1412 TCGA-13-1477 
       56.15        44.94        29.98        13.81         5.33        54.64 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1507 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
       20.68        22.39         4.77         3.09        14.24        12.23 
TCGA-13-2060 TCGA-20-0996 TCGA-20-1683 TCGA-23-1022 TCGA-23-1114 TCGA-23-1809 
        8.61        72.20        25.38        42.54        68.68         0.53 
TCGA-23-2079 TCGA-24-1419 TCGA-24-1474 TCGA-24-1553 TCGA-24-1556 TCGA-24-1565 
       91.66         7.86        22.22        58.09        70.62        10.26 
TCGA-24-1845 TCGA-24-1924 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
        3.81        30.21        28.18        44.52        57.07        36.16 
TCGA-24-2262 TCGA-24-2289 TCGA-25-1623 TCGA-25-1626 TCGA-25-1878 TCGA-25-2397 
        0.36        67.36        18.58        15.81        85.05        12.00 
TCGA-25-2408 TCGA-29-1690 TCGA-29-1702 TCGA-29-1710 TCGA-29-1763 TCGA-29-1766 
       31.00        44.71        18.67        29.23        66.81        39.12 
TCGA-29-1774 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1862 
       17.33         4.90        11.47         9.76        21.04         6.12 
TCGA-36-1569 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2540 
       29.10        25.74        27.85        24.23        24.69        23.80 
TCGA-36-2542 TCGA-36-2552 TCGA-42-2588 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 
       21.60        11.47         9.44        22.32        29.00        25.02 
TCGA-59-2349 TCGA-59-2352 TCGA-61-1721 TCGA-61-1722 TCGA-61-1900 TCGA-61-1904 
       80.12         9.40        11.11         8.09         5.79         9.07 
TCGA-61-1911 TCGA-61-2009 TCGA-61-2017 TCGA-61-2018 TCGA-61-2092 
       42.51        39.85        45.96        45.40        51.72 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.26               0.36 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            180.20              91.66 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             28.64              25.38 
[1] "0.3 - 180.2 (28.6)" "0.4 - 91.7 (25.4)" 
[1] "hr=" "1"  
D70V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  17P LOSS MUTATED         2   462                1
  17P LOSS WILD-TYPE       0    95                1
D70V3, multiclass
                  clus
vv                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  OMENTUM                         2                  0
  OVARY                         462                 95
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V4, continuous
D70V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     2 471
  17P LOSS WILD-TYPE   1  97
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2  471
  17P LOSS WILD-TYPE    1   97
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 2                  1
  YES              471                 97
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   10 23  4  3
  17P LOSS WILD-TYPE  4  3  1  0
D70V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               10                  4
  R1               23                  3
  R2                4                  1
  RX                3                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  3    15
  17P LOSS WILD-TYPE                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P LOSS MUTATED                          29
  17P LOSS WILD-TYPE                         3
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           1   391
  17P LOSS WILD-TYPE                                         0    84
D70V7, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                   15                  3
  BLACK OR AFRICAN AMERICAN                               29                  3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  391                 84
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     7 271
  17P LOSS WILD-TYPE   3  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7  271
  17P LOSS WILD-TYPE    3   54
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                  3
  NOT HISPANIC OR LATINO              271                 54
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED   175 192
  17Q LOSS WILD-TYPE  91  98
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               367                189 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               192                 98 
$`17Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 
       40.24        41.00        46.62        11.87        63.09        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 
       21.57        63.98        65.46        32.52        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       71.47        82.39        19.99        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       48.89        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       47.70        45.37        29.16         9.47        57.76        17.98 
TCGA-09-1659 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
        9.99        74.93        57.60        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 
       17.98         5.85         3.02        97.55         6.12        35.15 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-10-0926 
      112.41        71.11        39.75        20.94        26.93        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       81.47        18.51        33.24        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0758 TCGA-13-0762 TCGA-13-0766 
       44.55        39.58         2.73        11.38        32.25        21.40 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       38.93        28.70        19.59         8.71         7.79         8.28 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       43.86        35.28        35.28        68.94       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0901 
       74.27        66.67        67.99        69.01        43.36        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        47.84        44.84        37.08        27.72 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       21.17        14.89         4.64         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 
        7.36         6.05         6.84         4.70         4.21        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       61.71        98.04        70.82        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       49.25        54.31        38.40        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2059 
        4.21         4.41         4.18         2.56         3.91        12.23 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       10.78         8.75         6.28         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       26.20        27.52        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       47.54        15.39        26.83         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1111 TCGA-23-1113 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 
        2.24         3.22        31.20       129.96         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 
       33.47        58.13        24.95       115.89        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0979 TCGA-24-0980 
        2.76         4.70         4.50        19.66        41.56         7.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       22.32        54.12        63.55        47.41         6.31         6.38 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 
        7.99         0.76         6.25         6.02         5.95         4.83 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 
       17.39        28.37        19.17        18.67         8.55        72.92 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 
       45.14       105.99         9.11         3.45         1.18        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1557 
       57.40        16.21        41.06        51.91        88.50        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 
       19.53        44.09        45.50        47.70        25.87        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1846 TCGA-24-1847 
       88.37        48.33        38.24         8.32         4.37        11.28 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 
        5.79         9.80        22.68        30.21        11.05        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
        4.87        44.84        34.82        14.43        53.95        18.48 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       64.01        57.07        47.54        70.45        44.61         0.82 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 
       36.23        16.64        33.11        55.86         1.02        26.96 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 
       51.06        37.02         1.02        34.98        36.95        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
        2.99        12.00        18.02         0.36        20.61         7.86 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        56.94        60.59        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       24.99        18.05        49.05        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-29-1688 TCGA-29-1691 
       45.01        19.99        42.02        29.03        78.90        47.18 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1761 TCGA-29-1762 
       16.90        59.67        18.25        41.98        17.00        85.68 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 
       66.81        62.93        22.98        24.36        22.55        12.36 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       11.84        12.30        14.93         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       34.62        65.00        62.47         4.90        42.25        11.84 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       38.07        51.91        36.26         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 
       48.10        44.91        34.78        36.62        57.57        24.26 
TCGA-30-1891 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 
       30.05        18.77         6.71        42.51        44.12        28.77 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-2529 TCGA-36-2530 
       22.85         8.55        30.08        25.74        35.05        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2543 TCGA-36-2544 
       29.49        29.82        25.91        25.08         2.24        20.98 
TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 
       18.31        14.17         6.05        16.18         7.99        26.04 
TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       23.74        42.02         7.46        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1993 TCGA-59-2348 TCGA-59-2351 TCGA-59-2355 TCGA-59-2372 
       21.14        25.08       180.20       116.12         2.14        44.81 
TCGA-59-A5PD TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       20.52        20.94        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       31.79        28.47         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        8.42        11.41        13.02         9.07        34.13        31.30 
TCGA-61-1910 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       37.05        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 
        5.52         4.01        30.64         1.18        45.40         4.80 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 
        4.77        71.74        60.62        55.50        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56Q TCGA-VG-A8LO 
       44.52       125.75        22.22        31.07        18.94         0.79 
TCGA-WR-A838 
        8.05 

$`17Q LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1346 TCGA-04-1356 
        1.81        49.15         2.01        18.51        65.52        49.28 
TCGA-04-1362 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-09-0369 
       44.32        56.55        41.59        38.37       119.08        35.57 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 
       38.43        89.33        41.62         8.55         6.18         4.54 
TCGA-09-2051 TCGA-09-2056 TCGA-10-0925 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       63.09        12.46        54.31        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       35.44        35.80        15.12        12.39        31.10        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 
       17.82        55.17         2.50        11.18        11.54        34.06 
TCGA-13-0764 TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 TCGA-13-0800 TCGA-13-0802 
       31.04         8.45        36.72        30.35         8.12         8.19 
TCGA-13-0807 TCGA-13-0888 TCGA-13-0889 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       13.61        70.39        61.84        57.47        56.15        57.07 
TCGA-13-0906 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 TCGA-13-0923 TCGA-13-1408 
       44.94        34.06        29.98        13.81         6.41         5.92 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 
        5.33        54.64        29.42        20.68        22.39        82.88 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1507 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 
        4.24        37.61         4.77         3.09        14.24         8.61 
TCGA-13-A5FT TCGA-20-0996 TCGA-20-1683 TCGA-23-1022 TCGA-23-1023 TCGA-23-1027 
       54.77        72.20        25.38        42.54        40.54        31.76 
TCGA-23-1028 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       49.41        51.35        54.51        68.68         4.57        33.30 
TCGA-23-1118 TCGA-23-1120 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 TCGA-24-0966 
       86.01         4.27         0.53        87.48        91.66         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-1417 TCGA-24-1419 TCGA-24-1426 TCGA-24-1435 
       11.64        21.80         7.82         7.86         5.36        43.53 
TCGA-24-1464 TCGA-24-1474 TCGA-24-1546 TCGA-24-1549 TCGA-24-1552 TCGA-24-1553 
       12.46        22.22        64.27        56.58        41.39        58.09 
TCGA-24-1556 TCGA-24-1565 TCGA-24-1567 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       70.62        10.26        17.23         3.48         3.72         3.81 
TCGA-24-1850 TCGA-24-1927 TCGA-24-2020 TCGA-24-2024 TCGA-24-2027 TCGA-24-2035 
        5.52        16.44       152.02        58.16       109.71        28.18 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2289 
       44.52        36.16         0.79         0.36        31.63        67.36 
TCGA-24-2298 TCGA-25-1314 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 
       53.26        32.02        65.00         2.96        18.58        15.81 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 
       85.05        13.02         1.02         2.96        31.00        26.99 
TCGA-29-1690 TCGA-29-1699 TCGA-29-1702 TCGA-29-1710 TCGA-29-1711 TCGA-29-1766 
       44.71         0.53        18.67        29.23        34.62        39.12 
TCGA-29-1768 TCGA-29-1774 TCGA-29-2414 TCGA-29-2428 TCGA-29-2434 TCGA-29-2436 
       31.23        17.33        86.17        45.11        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1862 TCGA-30-1867 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       21.04         6.12         1.22        48.79        45.57        30.18 
TCGA-31-1951 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 
       22.49         2.20        29.10        21.53        22.55        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2540 TCGA-36-2542 TCGA-36-2547 TCGA-36-2552 
       24.23        24.69        23.80        21.60        20.52        11.47 
TCGA-42-2588 TCGA-42-2593 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 
        9.44         1.48         1.74        22.32        29.00        25.02 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 
       80.12        22.32         9.40        34.39         5.42        11.11 
TCGA-61-1722 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1900 TCGA-61-1911 
        8.09        48.79        44.84        35.80         5.79        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 
       48.92        56.61        14.50        17.98        30.64        39.85 
TCGA-61-2017 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2102 
       45.96        51.72        61.64        58.39        65.52         6.48 
TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P 
        6.35         8.61        39.68 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.26               0.36 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            180.20             152.02 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             27.88              28.18 
[1] "0.3 - 180.2 (27.9)" "0.4 - 152.0 (28.2)"
[1] "hr=" "1"  
D71V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  17Q LOSS MUTATED         2   368                1
  17Q LOSS WILD-TYPE       0   189                1
D71V3, multiclass
                  clus
vv                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  OMENTUM                         2                  0
  OVARY                         368                189
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V4, continuous
D71V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3 376
  17Q LOSS WILD-TYPE   0 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3  376
  17Q LOSS WILD-TYPE    0  192
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 3                  0
  YES              376                192
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  17Q LOSS MUTATED    8 19  2  2
  17Q LOSS WILD-TYPE  6  7  3  1
D71V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                8                  6
  R1               19                  7
  R2                2                  3
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  1    11
  17Q LOSS WILD-TYPE                                2     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q LOSS MUTATED                          22
  17Q LOSS WILD-TYPE                        10
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           1   315
  17Q LOSS WILD-TYPE                                         0   160
D71V7, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                   11                  7
  BLACK OR AFRICAN AMERICAN                               22                 10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  315                160
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4 217
  17Q LOSS WILD-TYPE   6 108
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4  217
  17Q LOSS WILD-TYPE    6  108
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              217                108
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    97 129
  18P LOSS WILD-TYPE 169 161
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               226                330 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               129                161 
$`18P LOSS MUTATED`
TCGA-04-1338 TCGA-04-1350 TCGA-04-1351 TCGA-04-1362 TCGA-04-1364 TCGA-04-1514 
       46.62        63.98        65.46        44.32        33.67        56.55 
TCGA-04-1517 TCGA-04-1530 TCGA-04-1649 TCGA-04-1651 TCGA-04-1655 TCGA-09-0367 
       19.99       119.08        64.64        36.23        45.37        17.98 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1672 TCGA-09-1673 TCGA-09-2044 TCGA-09-2053 
       57.60        61.87         5.85         3.02         6.12        39.75 
TCGA-09-2054 TCGA-10-0926 TCGA-10-0927 TCGA-10-0931 TCGA-13-0714 TCGA-13-0720 
       20.94        25.91        81.47        32.28         6.21        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 
       39.58         2.73        12.39        31.10        15.19        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 TCGA-13-0766 
        2.50        11.18        11.38        11.54        31.04        21.40 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 
       36.72        28.70        30.35         8.12        43.86        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0891 TCGA-13-0903 TCGA-13-0910 
       13.61        68.94       107.18        69.01        47.38        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1409 
       27.72        34.06         6.08        10.88         7.36         6.84 
TCGA-13-1411 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1495 
        4.21        29.42        98.04        22.39        70.82        49.25 
TCGA-13-1498 TCGA-13-1506 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-20-0990 
       37.61         4.41        10.78         8.75         6.28        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1021 
       26.20        27.52        25.38        19.10         2.66        47.54 
TCGA-23-1027 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       31.76         3.22        31.20         4.57        33.30        86.01 
TCGA-23-1122 TCGA-23-2072 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
       39.09        24.95        91.66        49.84         2.76         4.70 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1413 
        7.63        11.64        41.56        22.32        63.55         6.31 
TCGA-24-1416 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 TCGA-24-1431 TCGA-24-1436 
        6.38         6.25         5.95         4.83        19.17         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 
       72.92        12.46         3.45         1.18        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1551 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 
       64.27        16.21        51.91        70.62        39.88        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 TCGA-24-1614 TCGA-24-1842 
       45.50        47.70        25.87        90.15        48.33         8.32 
TCGA-24-1843 TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 
        3.48        11.28         5.79         9.80        22.68        16.44 
TCGA-24-1928 TCGA-24-2023 TCGA-24-2027 TCGA-24-2260 TCGA-24-2267 TCGA-24-2271 
       11.05        44.84       109.71        36.16        47.54        31.63 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 
       70.45         0.82        16.64        53.26        26.96        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1626 
       37.02         1.02        36.95         2.99         2.96        15.81 
TCGA-25-1627 TCGA-25-1630 TCGA-25-1632 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 
        0.36         7.86        56.94        35.54        18.05        85.05 
TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 
       13.02         1.02        38.04        45.01         2.96        29.03 
TCGA-25-2409 TCGA-29-1691 TCGA-29-1694 TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 
       26.99        47.18        38.53        31.20        16.90        59.67 
TCGA-29-1707 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 
       41.98        85.68        66.81        62.93        31.23        24.36 
TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 
       12.36        12.30         7.23        86.17        62.47        45.11 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1860 
       21.04        38.07        51.91         2.47        15.68        44.91 
TCGA-30-1861 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-36-1568 
       34.78        57.57        30.05        48.79        30.18        28.77 
TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 
       29.10        22.85         8.55        25.74        24.23        33.01 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 
       29.49        29.82        21.60         2.24        18.31        14.17 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1585 
       11.47        23.74        40.77         1.48        24.03         1.74 
TCGA-57-1993 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 
       25.08        22.32       116.12        34.39         5.42        44.81 
TCGA-59-A5PD TCGA-61-1727 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1904 
       20.52        18.54        33.67        43.69         1.45         9.07 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 
       38.17         2.01         5.52        17.98        39.85        30.64 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
        4.77        71.74        65.52        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 
       20.68        44.52         6.35        31.07 

$`18P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 
       40.24        41.00         1.81        49.15         2.01        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1356 
       11.87        65.52        63.09        48.76        21.57        49.28 
TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 
       32.52        76.57        71.47        82.39        41.59        38.37 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       29.10        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 
       31.86        47.70        29.16         9.47        57.76        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1668 
        9.99        38.43        89.33        74.93        41.62        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 
       30.51        17.98         8.55        97.55         6.18        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2055 TCGA-09-2056 
        4.54       112.41        71.11        63.09        26.93        12.46 
TCGA-10-0925 TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       54.31        18.51        33.24        11.70         3.91        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0730 TCGA-13-0761 
       35.80        15.12        19.86        24.59        17.82        34.06 
TCGA-13-0762 TCGA-13-0768 TCGA-13-0791 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       32.25         8.45        38.93        19.59         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0805 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
        8.28         8.19        35.28        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       70.39        61.84        67.99        43.36        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       57.07        19.36        48.33        47.84        44.94        44.84 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       29.98        21.17        14.89        13.81         4.64         6.41 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
        6.61         6.05         5.92         4.70         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       87.06        61.71        20.68        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       38.20         4.24        54.31        38.40        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       16.57         4.21         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-A5FT TCGA-13-A5FU 
        3.09        14.24        12.23         8.61        54.77         8.42 
TCGA-20-0987 TCGA-20-0996 TCGA-20-1685 TCGA-20-1686 TCGA-23-1022 TCGA-23-1023 
       23.05        72.20        16.70         2.93        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       15.39        26.83        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 TCGA-23-1119 TCGA-23-1120 
        2.24        51.35        54.51        68.68       129.96         4.27 
TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 
        6.38        33.47        58.13         0.53       115.89        87.48 
TCGA-23-2081 TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 
       77.00         4.50        19.66        21.80         7.66        54.12 
TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 
       47.41         7.82         7.99         7.86         0.76         6.02 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1466 
        5.36        17.39        28.37        18.67        43.53        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1474 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 
      105.99         9.11        22.22        56.58        41.06        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1558 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 
       58.09        88.50        19.53        10.26        17.23        88.37 
TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1850 TCGA-24-1924 
       38.24         3.72         3.81         4.37         5.52        30.21 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 
       81.11         4.87       152.02        58.16        34.82        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       53.95        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 
        0.79         0.36        44.61        67.36        36.23        33.11 
TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 
       55.86         1.02        32.02        34.98        65.00        33.96 
TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 
       12.00        18.58        18.02        20.61         0.30        60.59 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 
       51.22        14.96        24.99        49.05         3.02        12.00 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
       19.99        42.02        31.00        78.90        44.71       101.79 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1705 
        0.79        33.70        68.32         0.53        18.67        18.25 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1766 TCGA-29-1769 TCGA-29-1771 
       29.23        34.62        17.00        39.12        22.98        22.55 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 
       17.33        11.84        14.93         8.38         5.36        34.62 
TCGA-29-2425 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       65.00         4.90        42.25        11.84        11.47         9.76 
TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       36.26         0.26        48.10         6.12        36.62         1.22 
TCGA-30-1887 TCGA-31-1944 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       24.26        45.57        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-31-1959 TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 
       44.12         2.20        21.53        22.55        30.08        27.85 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 
       24.69        35.05        25.91        25.08        23.80        20.98 
TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 
       20.52         6.05        16.18         7.99        26.04         9.44 
TCGA-42-2589 TCGA-42-2590 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 
       42.02         7.46        11.38        21.14        22.32        29.00 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2352 TCGA-59-2355 TCGA-61-1721 
       25.02       180.20        80.12         9.40         2.14        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
        8.09        20.94        31.43        27.88         4.34        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1899 
       28.47        48.79        44.84        35.80         2.43         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
        5.79        11.41        13.02        34.13        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       42.51        48.92        56.61        67.76        43.43        15.75 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       14.50         4.01        30.64         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2111 
        4.80        51.72        61.64        58.39        60.62       125.75 
TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       22.22         8.61        39.68        18.94         0.79         8.05 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.36               0.26 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            119.08             180.20 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             28.21              28.03 
[1] "0.4 - 119.1 (28.2)" "0.3 - 180.2 (28.0)"
[1] "hr=" "1.2"
D72V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18P LOSS MUTATED         1   227                0
  18P LOSS WILD-TYPE       1   330                2
D72V3, multiclass
                  clus
vv                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         227                330
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V4, continuous
D72V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3 228
  18P LOSS WILD-TYPE   0 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3  228
  18P LOSS WILD-TYPE    0  340
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 3                  0
  YES              228                340
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED    6 13  1  0
  18P LOSS WILD-TYPE  8 13  4  3
D72V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0                6                  8
  R1               13                 13
  R2                1                  4
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  3     6
  18P LOSS WILD-TYPE                                0    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED                           8
  18P LOSS WILD-TYPE                        24
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           1   195
  18P LOSS WILD-TYPE                                         0   280
D72V7, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                    6                 12
  BLACK OR AFRICAN AMERICAN                                8                 24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  195                280
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     4 129
  18P LOSS WILD-TYPE   6 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4  129
  18P LOSS WILD-TYPE    6  196
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              129                196
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   130 151
  18Q LOSS WILD-TYPE 136 139
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               281                275 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               151                139 
$`18Q LOSS MUTATED`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1347 TCGA-04-1350 
       41.00         1.81        49.15        46.62        63.09        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1517 
       65.46        49.28        32.52        44.32        33.67        19.99 
TCGA-04-1530 TCGA-04-1649 TCGA-04-1651 TCGA-04-1655 TCGA-09-0367 TCGA-09-1666 
      119.08        64.64        36.23        45.37        17.98        57.60 
TCGA-09-1667 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       61.87         5.85         3.02        97.55         6.18         6.12 
TCGA-09-2048 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 TCGA-10-0926 
        4.54        71.11        39.75        20.94        12.46        25.91 
TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 
       81.47        33.24        32.28         6.21        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
        2.73        12.39        31.10        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 TCGA-13-0766 
        2.50        11.18        11.38        11.54        31.04        21.40 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 
       36.72        28.70        30.35         8.12        43.86        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0899 TCGA-13-0903 
       13.61        68.94       107.18        74.27        56.15        47.38 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
        6.08        10.88         7.36         6.05         5.92         6.84 
TCGA-13-1411 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1495 
        4.21        29.42        98.04        22.39        70.82        49.25 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1505 TCGA-13-1506 TCGA-13-2059 
       37.61        38.40        13.97         4.21         4.41        12.23 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       10.78         8.75         6.28        23.05        25.94        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       27.52        25.38        19.10        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1032 TCGA-23-1111 
       47.54        40.54        31.76        49.41         2.24         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 
       31.20         4.57        33.30        86.01       129.96        39.09 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       58.13        24.95        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 
        4.70         7.63        11.64        41.56        22.32        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1423 
       47.41         6.31         6.38         7.82         7.99         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1436 TCGA-24-1463 
        6.02         5.95         4.83        17.39         8.55        72.92 
TCGA-24-1464 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       12.46         3.45         1.18        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1552 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       64.27        16.21        41.39        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1603 TCGA-24-1614 
       44.09        45.50        47.70        25.87        90.15        48.33 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        8.32         3.48         3.72        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-2020 TCGA-24-2023 
        9.80        22.68        16.44        11.05       152.02        44.84 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
      109.71        14.43        28.18        36.16         0.79        47.54 
TCGA-24-2271 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2298 TCGA-25-1312 
       31.63         0.82        67.36        16.64        53.26         1.02 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1321 TCGA-25-1322 
       26.96        51.06        37.02         1.02        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1632 
       12.00         2.96        18.02        15.81         0.36        56.94 
TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 
       35.54        18.05        85.05        13.02         1.02        38.04 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1691 TCGA-29-1694 TCGA-29-1697 
        2.96        29.03        26.99        47.18        38.53        31.20 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1762 TCGA-29-1763 
       16.90        18.67        59.67        41.98        85.68        66.81 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 
       62.93        31.23        24.36        12.36        12.30         8.38 
TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2434 
        7.23        86.17        65.00        62.47        45.11        11.47 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1861 
       21.04        38.07        51.91         2.47        15.68        34.78 
TCGA-30-1866 TCGA-30-1880 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1959 
       36.62        57.57        30.05        45.57        30.18         2.20 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       29.10        21.53        22.85         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 
       27.85        24.23        29.49        29.82        25.08        21.60 
TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-36-2552 TCGA-42-2587 TCGA-42-2591 
        2.24        18.31        14.17        11.47        23.74        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 
        1.48        24.03        11.38         1.74        29.00        25.08 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1730 TCGA-61-1737 TCGA-61-1741 
       44.81        20.52        20.94         4.34        44.84        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1904 TCGA-61-1906 TCGA-61-1995 TCGA-61-2002 
       43.69         1.45         9.07        34.13         2.01        17.98 
TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 
       30.64         4.77        71.74        60.62         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 TCGA-WR-A838 
       20.68        44.52         6.35        31.07         8.05 

$`18Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 
       40.24         2.01        18.51        11.87        65.52        48.76 
TCGA-04-1349 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       21.57        76.57        71.47        82.39        56.55        41.59 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37        29.10        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       28.64        31.86        47.70        29.16         9.47        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       35.57         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-2045 TCGA-09-2049 
       55.36        30.51        17.98         8.55        35.15       112.41 
TCGA-09-2051 TCGA-09-2055 TCGA-10-0925 TCGA-10-0928 TCGA-10-0933 TCGA-10-0934 
       63.09        26.93        54.31        18.51        11.70         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0761 
       35.44        35.80        15.12        19.86        24.59        34.06 
TCGA-13-0762 TCGA-13-0768 TCGA-13-0791 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       32.25         8.45        38.93        19.59         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0805 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
        8.28         8.19        35.28        91.40        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 
       61.84        67.99        69.01        43.36        57.47        57.07 
TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       19.36        48.33        47.84        21.17        14.89        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-1404 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
        4.64         6.41         6.61         4.70         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       87.06        61.71        20.68        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1501 TCGA-13-1504 TCGA-13-1507 
       38.20         4.24        54.31        32.84        16.57         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 
        4.18         2.56         3.91         3.09        14.24         8.61 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0996 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 
       54.77         8.42        72.20        42.54        15.39        26.83 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 
        8.81        29.13        18.90        51.35        54.51        68.68 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 
        4.27         6.38        33.47         0.53       115.89        87.48 
TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1419 
        4.50        19.66        21.80         7.66        54.12         7.86 
TCGA-24-1422 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        0.76         5.36        28.37        19.17        18.67        43.53 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       45.14       105.99         9.11        56.58        41.06        51.91 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1616 
       58.09        88.50        10.26        17.23        88.37        38.24 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 TCGA-24-2024 
        3.81         4.37        30.21        81.11         4.87        58.16 
TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       34.82        53.95        18.48        64.01        44.52        57.07 
TCGA-24-2262 TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 
        0.36        70.45        44.61        36.23        33.11        55.86 
TCGA-25-1314 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1623 TCGA-25-1628 
       32.02        34.98        65.00        36.95        18.58        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
        7.86         0.30        60.59        51.22        14.96        24.99 
TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       49.05         3.02        12.00        45.01        19.99        42.02 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1695 TCGA-29-1696 
       31.00        78.90        44.71       101.79         0.79        33.70 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       68.32         0.53        18.25        29.23        34.62        17.00 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 
       39.12        22.98        22.55        17.33        11.84        14.93 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 
        5.36        34.62         4.90        42.25        11.84         9.76 
TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 
       36.26         0.26        48.10        44.91         6.12         1.22 
TCGA-30-1887 TCGA-30-1892 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       24.26        48.79        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1574 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       44.12        28.77        22.55        24.69        35.05        33.01 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 
       25.91        23.80        20.98        20.52         6.05        16.18 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-57-1584 
        7.99        26.04         9.44        42.02         7.46        21.14 
TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-61-1721 TCGA-61-1722 
       22.32        25.02       180.20        80.12        11.11         8.09 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       31.43        18.54        27.88        31.79        28.47        48.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       35.80         2.43         8.42         5.79        11.41        13.02 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       31.30        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 
       43.43        15.75        38.17         5.52        14.50         4.01 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       30.64        39.85         1.18        45.96        45.40         4.80 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2111 
       51.72        61.64        58.39        65.52        55.50       125.75 
TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       22.22         8.61        39.68        18.94         0.79 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.36               0.26 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            152.02             180.20 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             25.91              30.21 
[1] "0.4 - 152.0 (25.9)" "0.3 - 180.2 (30.2)"
[1] "hr=" "1.2"
D73V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  18Q LOSS MUTATED         1   282                0
  18Q LOSS WILD-TYPE       1   275                2
D73V3, multiclass
                  clus
vv                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         282                275
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V4, continuous
D73V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3 286
  18Q LOSS WILD-TYPE   0 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3  286
  18Q LOSS WILD-TYPE    0  282
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 3                  0
  YES              286                282
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS MUTATED    7 14  1  0
  18Q LOSS WILD-TYPE  7 12  4  3
D73V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0                7                  7
  R1               14                 12
  R2                1                  4
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  3     6
  18Q LOSS WILD-TYPE                                0    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q LOSS MUTATED                          13
  18Q LOSS WILD-TYPE                        19
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           1   242
  18Q LOSS WILD-TYPE                                         0   233
D73V7, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                    6                 12
  BLACK OR AFRICAN AMERICAN                               13                 19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  242                233
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     7 158
  18Q LOSS WILD-TYPE   3 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      7  158
  18Q LOSS WILD-TYPE    3  167
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                  3
  NOT HISPANIC OR LATINO              158                167
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    86  93
  19P LOSS WILD-TYPE 180 197
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               179                377 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                93                197 
$`19P LOSS MUTATED`
TCGA-04-1332 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       41.00        11.87        63.09        21.57        63.98        49.28 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 
       44.32        33.67        76.57        71.47        82.39        41.59 
TCGA-04-1517 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1654 
       19.99       119.08        55.43        48.89        27.88        47.70 
TCGA-04-1655 TCGA-09-0366 TCGA-09-1659 TCGA-09-1661 TCGA-09-1668 TCGA-09-1672 
       45.37        57.76         9.99        38.43        55.36         5.85 
TCGA-09-1673 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 
        3.02       112.41        63.09        39.75        26.93        12.46 
TCGA-10-0928 TCGA-10-0936 TCGA-10-0937 TCGA-13-0723 TCGA-13-0724 TCGA-13-0730 
       18.51        35.80        15.12        39.58         2.73        17.82 
TCGA-13-0762 TCGA-13-0768 TCGA-13-0800 TCGA-13-0803 TCGA-13-0885 TCGA-13-0886 
       32.25         8.45         8.12        43.86        91.40        74.27 
TCGA-13-0899 TCGA-13-0908 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       56.15        44.84        27.72        14.89         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1411 TCGA-13-1412 
        6.08        10.88         6.61         7.36         4.21         5.33 
TCGA-13-1483 TCGA-13-1489 TCGA-13-1492 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 
       29.42        82.88        73.55         4.24        37.61        38.40 
TCGA-13-1504 TCGA-13-1507 TCGA-13-2060 TCGA-13-2061 TCGA-23-1027 TCGA-23-1030 
       16.57         4.77         8.61        10.78        31.76        29.13 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1113 TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 
        2.24        54.51        31.20       129.96         4.27        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0979 
       58.13        24.95         4.70         7.63        19.66        41.56 
TCGA-24-1413 TCGA-24-1424 TCGA-24-1434 TCGA-24-1463 TCGA-24-1464 TCGA-24-1470 
        6.31         6.02        18.67        72.92        12.46         3.45 
TCGA-24-1544 TCGA-24-1549 TCGA-24-1560 TCGA-24-1564 TCGA-24-1565 TCGA-24-1846 
       26.96        56.58        44.09        25.87        10.26         4.37 
TCGA-24-2019 TCGA-24-2024 TCGA-24-2026 TCGA-24-2260 TCGA-24-2288 TCGA-24-2290 
        4.87        58.16        34.82        36.16         0.82        36.23 
TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1316 TCGA-25-1317 TCGA-25-1627 
       16.64        53.26        26.96        37.02         1.02         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       20.61         7.86        56.94        60.59        35.54        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2393 
       14.96        24.99        18.05        85.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-29-1691 TCGA-29-1696 
        3.02        19.99        42.02        29.03        47.18        33.70 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
       31.20         0.53        16.90        18.25        41.98        29.23 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1778 
       17.00        66.81        22.98        22.55        17.33        14.93 
TCGA-29-2427 TCGA-29-2428 TCGA-30-1853 TCGA-30-1861 TCGA-30-1866 TCGA-30-1891 
       62.47        45.11        36.26        34.78        36.62        30.05 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
        6.71        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1581 TCGA-36-2530 TCGA-36-2537 
       22.85         8.55        30.08        24.69        33.01        25.91 
TCGA-36-2538 TCGA-36-2548 TCGA-36-2551 TCGA-3P-A9WA TCGA-57-1584 TCGA-57-1585 
       25.08        14.17        16.18         7.99        21.14         1.74 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1733 
       25.08        25.02        44.81        20.52         8.09        31.79 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1903 TCGA-61-1907 TCGA-61-1915 TCGA-61-1917 
       35.80         2.43        13.02        31.30        67.76        43.43 
TCGA-61-1919 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 
       38.17        17.98         1.18        45.96         4.80         4.77 
TCGA-61-2102 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
        6.48         6.35         8.61        39.68        18.94 

$`19P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24         1.81        49.15         2.01        46.62        18.51 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 TCGA-04-1361 TCGA-04-1514 TCGA-04-1525 
       65.52        48.76        65.46        32.52        56.55        38.37 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       29.10        84.20        28.64        64.64        36.23        31.86 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1662 TCGA-09-1664 
       29.16         9.47        17.98        35.57        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 
       41.62        57.60        61.87        30.51        17.98         8.55 
TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
       97.55         6.18         6.12        35.15         4.54        71.11 
TCGA-09-2054 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 
       20.94        54.31        25.91        81.47        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       11.70         3.91        35.44        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 
       44.55        12.39        31.10        15.19        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       11.18        11.38        11.54        34.06        31.04        21.40 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       38.93        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        7.79         8.28         8.19        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       68.94       107.18        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       69.01        43.36        57.47        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 
       48.33        47.84        44.94        37.08        34.06        29.98 
TCGA-13-0916 TCGA-13-0920 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       21.17        13.81         6.05         5.92         6.84         4.70 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       54.64        87.06        61.71        98.04        20.68        22.39 
TCGA-13-1488 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1500 
       70.82        52.44        38.20        49.25        54.31        13.97 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
       32.84         4.21         4.41         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
        3.09        14.24        12.23         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.42        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       25.38        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 
       42.54        40.54        15.39        26.83        49.41         8.81 
TCGA-23-1031 TCGA-23-1109 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       18.90        51.35         3.22        68.68         4.57        33.30 
TCGA-23-1118 TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 
       86.01         6.38        39.09         0.53       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0970 
       91.66        77.00        49.84         2.76         4.50        11.64 
TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       21.80         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.38         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        5.95         5.36         4.83        17.39        28.37        19.17 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 
       43.53         8.55        45.14       105.99         9.11         1.18 
TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 
       22.22        57.40        64.27        16.21        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       41.39        58.09        88.50        70.62        39.88        19.53 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       45.50        47.70        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 
       38.24         8.32         3.48         3.72         3.81        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
        5.79         5.52         9.80        22.68        30.21        16.44 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 
       11.05        81.11       152.02        44.84       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 
       53.95        18.48        28.18        64.01        44.52        57.07 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
        0.79         0.36        47.54        31.63        70.45        44.61 
TCGA-24-2289 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 
       67.36        33.11        55.86         1.02        32.02        51.06 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        36.95        33.96         2.99        12.00 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1631 TCGA-25-2042 
        2.96        18.58        18.02        15.81         0.30        13.02 
TCGA-25-2391 TCGA-25-2397 TCGA-25-2398 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 
       49.05        12.00        45.01         2.96        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1698 
       78.90        44.71       101.79        38.53         0.79        68.32 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 
       18.67        59.67        34.62        85.68        62.93        39.12 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       31.23        24.36        12.36        11.84        12.30         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2429 
        7.23         5.36        34.62        86.17        65.00         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        11.84        11.47         9.76        21.04        38.07 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       51.91         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
        6.12         1.22        57.57        24.26        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 
       30.18        18.77        22.49        21.53        22.55        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2540 
       27.85        24.23        35.05        29.49        29.82        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 
       21.60         2.24        20.98        18.31        20.52         6.05 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       11.47        26.04        23.74         9.44        42.02         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1992 
       40.77         1.48        24.03        11.38        22.32        29.00 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
      180.20        80.12        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        2.14         5.42        11.11        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 
       27.88         4.34        28.47        48.79        44.84        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 
       43.69         1.45         8.42         5.79        11.41         9.07 
TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 
       34.13        37.05        42.51        48.92        56.61        15.75 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        2.01         5.52        14.50         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2018 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       30.64        45.40        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        65.52        55.50        76.87        20.68        44.52 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 
      125.75        22.22        31.07         0.79         8.05 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.36               0.26 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            129.96             180.20 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             26.96              28.64 
[1] "0.4 - 130.0 (27.0)" "0.3 - 180.2 (28.6)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  19P LOSS MUTATED         2   179                0
  19P LOSS WILD-TYPE       0   378                2
D74V3, multiclass
                  clus
vv                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  OMENTUM                         2                  0
  OVARY                         179                378
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V4, continuous
D74V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0 184
  19P LOSS WILD-TYPE   3 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0  184
  19P LOSS WILD-TYPE    3  384
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 0                  3
  YES              184                384
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  19P LOSS MUTATED    3 11  1  2
  19P LOSS WILD-TYPE 11 15  4  1
D74V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                3                 11
  R1               11                 15
  R2                1                  4
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  1     3
  19P LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED                          12
  19P LOSS WILD-TYPE                        20
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           0   156
  19P LOSS WILD-TYPE                                         1   319
D74V7, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                               12                 20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  156                319
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     4 106
  19P LOSS WILD-TYPE   6 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4  106
  19P LOSS WILD-TYPE    6  219
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              106                219
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    85  86
  19Q LOSS WILD-TYPE 181 204
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               171                385 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                86                204 
$`19Q LOSS MUTATED`
TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 
       63.09        21.57        63.98        49.28        44.32        33.67 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 
       76.57        71.47        82.39       119.08        55.43        48.89 
TCGA-04-1646 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-1659 TCGA-09-1664 
       27.88        47.70        45.37        57.76         9.99        74.93 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2049 
       61.87        55.36         5.85         3.02        97.55       112.41 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-10-0928 TCGA-10-0936 
       63.09        39.75        26.93        12.46        18.51        35.80 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0723 TCGA-13-0724 TCGA-13-0762 TCGA-13-0768 
       15.12        19.86        39.58         2.73        32.25         8.45 
TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 TCGA-13-0807 TCGA-13-0886 TCGA-13-0899 
        8.12        43.86        35.28        13.61        74.27        56.15 
TCGA-13-0908 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 
       44.84        27.72        14.89         4.64         6.41        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 TCGA-13-1412 TCGA-13-1489 
        6.61         7.36         6.05         4.21         5.33        82.88 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1510 TCGA-13-2060 
       38.20         4.24        37.61        38.40         2.56         8.61 
TCGA-13-2061 TCGA-20-1686 TCGA-23-1021 TCGA-23-1024 TCGA-23-1030 TCGA-23-1032 
       10.78         2.93        47.54        15.39        29.13         2.24 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 
       54.51        31.20       129.96         4.27        33.47        58.13 
TCGA-23-2072 TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0979 TCGA-24-0980 
       24.95         4.70         7.63        19.66        41.56         7.66 
TCGA-24-0982 TCGA-24-1413 TCGA-24-1424 TCGA-24-1434 TCGA-24-1463 TCGA-24-1464 
       22.32         6.31         6.02        18.67        72.92        12.46 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1549 TCGA-24-1560 TCGA-24-1564 TCGA-24-1565 
      105.99         3.45        56.58        44.09        25.87        10.26 
TCGA-24-1846 TCGA-24-2019 TCGA-24-2024 TCGA-24-2026 TCGA-24-2260 TCGA-24-2290 
        4.37         4.87        58.16        34.82        36.16        36.23 
TCGA-24-2293 TCGA-24-2298 TCGA-25-1316 TCGA-25-1627 TCGA-25-1628 TCGA-25-1632 
       16.64        53.26        37.02         0.36        20.61        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       60.59        35.54        51.22        14.96        24.99        18.05 
TCGA-25-1878 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 
       85.05         1.02        38.04         3.02        19.99        42.02 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1705 TCGA-29-1707 
       38.53        33.70        31.20         0.53        18.25        41.98 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1769 TCGA-29-1771 TCGA-29-1778 
       29.23        17.00        66.81        22.98        22.55        14.93 
TCGA-29-2427 TCGA-29-2428 TCGA-30-1853 TCGA-30-1861 TCGA-30-1866 TCGA-30-1891 
       62.47        45.11        36.26        34.78        36.62        30.05 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 
        6.71        42.51        44.12        28.77        29.10        22.85 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2537 
        8.55        30.08        24.23        24.69        33.01        25.91 
TCGA-36-2538 TCGA-36-2548 TCGA-36-2551 TCGA-3P-A9WA TCGA-57-1584 TCGA-57-1585 
       25.08        14.17        16.18         7.99        21.14         1.74 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1725 TCGA-61-1733 
       25.08        25.02        44.81        20.52        31.43        31.79 
TCGA-61-1738 TCGA-61-1903 TCGA-61-1907 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 
       35.80        13.02        31.30        67.76        43.43        38.17 
TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2102 
       17.98         1.18        45.96         4.80         4.77         6.48 
TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q 
        6.35        39.68        18.94 

$`19Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 TCGA-04-1361 
       18.51        11.87        65.52        48.76        65.46        32.52 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 
       56.55        41.59        19.99        38.37        29.10        84.20 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-09-0364 TCGA-09-0365 
       28.64        64.64        36.23        31.86        29.16         9.47 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 
       17.98        35.57        38.43        89.33        41.62        57.60 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
       30.51        17.98         8.55         6.18         6.12        35.15 
TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
        4.54        71.11        20.94        54.31        25.91        81.47 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-13-0714 
       33.24        32.28        11.70         3.91        35.44         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       24.59        44.55        12.39        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       55.17         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       31.04        21.40        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0805 
       19.59         8.71         7.79         8.28         8.19        35.28 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       68.94       107.18        91.40        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 
       67.99        69.01        43.36        57.47        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 
       47.38        48.33        47.84        44.94        37.08        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0924 TCGA-13-1408 TCGA-13-1409 
       29.98        21.17        13.81         6.08         5.92         6.84 
TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        4.70        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 
       20.68        22.39        70.82        52.44        73.55        49.25 
TCGA-13-1497 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       54.31        13.97        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.77         4.18         3.91         3.09        14.24        12.23 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.75         6.28        54.77         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
       26.20        72.20        27.52        25.38        19.10        16.70 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
        2.66        42.54        40.54        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 
        8.81        18.90        51.35         3.22        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 TCGA-23-1122 TCGA-23-1809 TCGA-23-2077 
       33.30        86.01         6.38        39.09         0.53       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 
       87.48        91.66        77.00        49.84         2.76         4.50 
TCGA-24-0970 TCGA-24-0975 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 
       11.64        21.80        54.12        63.55        47.41         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 
        7.82         7.99         7.86         0.76         6.25         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 
        5.36         4.83        17.39        28.37        19.17        43.53 
TCGA-24-1436 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
        8.55        45.14         9.11         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        16.21        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1562 
       58.09        88.50        70.62        39.88        19.53        45.50 
TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       47.70        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 
        8.32         3.48         3.72         3.81        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
       81.11       152.02        44.84       109.71        14.43        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 
       18.48        28.18        64.01        44.52        57.07         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
        0.36        47.54        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       67.36        33.11        55.86         1.02        26.96        32.02 
TCGA-25-1315 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       51.06         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
        2.99        12.00         2.96        18.58        18.02        15.81 
TCGA-25-1630 TCGA-25-1631 TCGA-25-2042 TCGA-25-2391 TCGA-25-2397 TCGA-25-2398 
        7.86         0.30        13.02        49.05        12.00        45.01 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        2.96        29.03        31.00        26.99        78.90        44.71 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 
       47.18       101.79         0.79        68.32        16.90        18.67 
TCGA-29-1703 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       59.67        34.62        85.68        62.93        39.12        31.23 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       24.36        17.33        12.36        11.84        12.30         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2429 
        7.23         5.36        34.62        86.17        65.00         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        11.84        11.47         9.76        21.04        38.07 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       51.91         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
        6.12         1.22        57.57        24.26        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1959 TCGA-36-1570 TCGA-36-1574 
       30.18        18.77        22.49         2.20        21.53        22.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2540 
       25.74        27.85        35.05        29.49        29.82        23.80 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 
       21.60         2.24        20.98        18.31        20.52         6.05 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       11.47        26.04        23.74         9.44        42.02         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1992 
       40.77         1.48        24.03        11.38        22.32        29.00 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
      180.20        80.12        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 
        2.14         5.42        11.11         8.09        20.94        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 
       27.88         4.34        28.47        48.79        44.84         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       33.67        43.69         1.45         8.42         5.79        11.41 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 
        9.07        34.13        37.05        42.51        48.92        56.61 
TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 
       15.75         2.01         5.52        14.50         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2018 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       39.85        30.64        45.40        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 
       58.39        60.62        65.52        55.50        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-VG-A8LO 
       44.52       125.75        22.22        31.07         8.61         0.79 
TCGA-WR-A838 
        8.05 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.36               0.26 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            129.96             180.20 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             28.77              27.88 
[1] "0.4 - 130.0 (28.8)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1"  
D75V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  19Q LOSS MUTATED         2   170                0
  19Q LOSS WILD-TYPE       0   387                2
D75V3, multiclass
                  clus
vv                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  OMENTUM                         2                  0
  OVARY                         170                387
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V4, continuous
D75V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0 176
  19Q LOSS WILD-TYPE   3 392
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0  176
  19Q LOSS WILD-TYPE    3  392
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 0                  3
  YES              176                392
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  19Q LOSS MUTATED    2 11  1  2
  19Q LOSS WILD-TYPE 12 15  4  1
D75V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                2                 12
  R1               11                 15
  R2                1                  4
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     3
  19Q LOSS WILD-TYPE                                3    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q LOSS MUTATED                          11
  19Q LOSS WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           0   148
  19Q LOSS WILD-TYPE                                         1   327
D75V7, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                               11                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                  148                327
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     4 101
  19Q LOSS WILD-TYPE   6 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4  101
  19Q LOSS WILD-TYPE    6  224
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  6
  NOT HISPANIC OR LATINO              101                224
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    30  18
  20P LOSS WILD-TYPE 236 272
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                48                508 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                272 
$`20P LOSS MUTATED`
TCGA-04-1336 TCGA-04-1536 TCGA-09-0364 TCGA-09-1667 TCGA-09-2048 TCGA-10-0930 
       49.15        29.10        29.16        61.87         4.54        33.24 
TCGA-13-0720 TCGA-13-0804 TCGA-13-0883 TCGA-13-0893 TCGA-13-0921 TCGA-13-1489 
       44.55        35.28        68.94        43.36         4.64        82.88 
TCGA-13-1494 TCGA-13-1495 TCGA-13-2059 TCGA-13-2071 TCGA-20-0987 TCGA-20-1682 
       38.20        49.25        12.23         6.28        23.05        27.52 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1028 TCGA-23-1118 TCGA-23-1119 TCGA-23-2072 
        2.66        42.54        49.41        86.01       129.96        24.95 
TCGA-24-1417 TCGA-24-1426 TCGA-24-1428 TCGA-24-1463 TCGA-24-1471 TCGA-24-1552 
        7.82         5.36        17.39        72.92         1.18        41.39 
TCGA-24-1603 TCGA-24-2298 TCGA-25-2392 TCGA-29-1693 TCGA-29-1702 TCGA-29-1711 
       90.15        53.26         1.02       101.79        18.67        34.62 
TCGA-29-1781 TCGA-29-2434 TCGA-29-2436 TCGA-36-1577 TCGA-36-1578 TCGA-57-1993 
        8.38        11.47         9.76        25.74        27.85        25.08 
TCGA-61-1725 TCGA-61-1734 TCGA-61-1737 TCGA-61-1741 TCGA-61-2088 TCGA-WR-A838 
       31.43        28.47        44.84        33.67         4.77         8.05 

$`20P LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00         1.81         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       65.46        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       71.47        82.39        56.55        41.59        19.99        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
      119.08        84.20        55.43        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 
       64.64        36.23        31.86        47.70        45.37         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 
       74.93        41.62        57.60        55.36        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 
       35.15       112.41        71.11        63.09        39.75        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       32.28        11.70         3.91        35.44        35.80        15.12 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
       19.86         6.21        24.59        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.10        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       11.38        11.54        34.06        32.25        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
        8.45        38.93        36.72        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
        8.71         7.79         8.12         8.28         8.19        43.86 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       35.28        13.61       107.18        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 
       70.39        61.84        67.99        69.01        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       14.89        13.81         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        7.36         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 
       20.68        22.39        70.82        52.44        73.55         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       54.31        37.61        38.40        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.21         4.41         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
        3.09        14.24         8.61        10.78         8.75        54.77 
TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
        8.42        25.94        26.20        72.20        25.38        19.10 
TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       16.70         2.93        47.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       31.76         8.81        29.13        18.90         2.24        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       54.51         3.22        31.20        68.68         4.57        33.30 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
        4.27         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
      115.89        87.48        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.70         4.50         7.63        19.66        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
       41.56         7.66        22.32        54.12        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
        6.31         6.38         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        6.02         5.95         4.83        28.37        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
       43.53         8.55        12.46        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        3.45        22.22        26.96        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       56.58        41.06        51.91        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 
       39.88        19.53        44.09        45.50        47.70        25.87 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       10.26        17.23        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        3.48         3.72         3.81         4.37        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       81.11         4.87       152.02        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
      109.71        14.43        53.95        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       44.52        57.07        36.16         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
       31.63        70.45        44.61         0.82        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       16.64        33.11        55.86         1.02        26.96        32.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       51.06        37.02         1.02        34.98        65.00        36.95 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       33.96         2.99        12.00         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       15.81         0.36        20.61         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       60.59        35.54        51.22        14.96        24.99        18.05 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       85.05        13.02        49.05        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       45.01        19.99        42.02         2.96        29.03        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 
       26.99        78.90        44.71        47.18        38.53         0.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 
       33.70        31.20        68.32         0.53        16.90        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       18.25        41.98        29.23        17.00        85.68        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.12        31.23        22.98        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 
       17.33        12.36        11.84        12.30        14.93         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        5.36        34.62        86.17        65.00        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
        4.90        42.25        11.84        21.04        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       36.26         2.47        15.68         0.26        48.10        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       34.78         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       30.05        48.79        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
        6.71        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 
       21.53        22.85        22.55         8.55        30.08        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       24.69        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.08        23.80        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       20.52        14.17         6.05        16.18        11.47         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       26.04        23.74         9.44        42.02         7.46        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        1.48        24.03        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       29.00        25.02       180.20        80.12        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
        9.40        34.39         2.14         5.42        44.81        20.52 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       11.11         8.09        20.94        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 
       31.79        48.79        35.80         2.43        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       31.30        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       43.43        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       17.98         4.01        30.64        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96        45.40         4.80        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       58.39        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       20.68        44.52       125.75        22.22         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        8.61        39.68        18.94         0.79 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1.02               0.26 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            129.96             180.20 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             29.13              27.80 
[1] "1.0 - 130.0 (29.1)" "0.3 - 180.2 (27.8)"
[1] "hr=" "1.6"
D76V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20P LOSS MUTATED         0    48                0
  20P LOSS WILD-TYPE       2   509                2
D76V3, multiclass
                  clus
vv                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          48                509
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V4, continuous
D76V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  48
  20P LOSS WILD-TYPE   2 520
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   48
  20P LOSS WILD-TYPE    2  520
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 1                  2
  YES               48                520
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  20P LOSS MUTATED    3  0  0  0
  20P LOSS WILD-TYPE 11 26  5  3
D76V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                3                 11
  R1                0                 26
  R2                0                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     2
  20P LOSS WILD-TYPE                                3    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P LOSS MUTATED                           4
  20P LOSS WILD-TYPE                        28
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           0    42
  20P LOSS WILD-TYPE                                         1   433
D76V7, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    2                 16
  BLACK OR AFRICAN AMERICAN                                4                 28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   42                433
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  30
  20P LOSS WILD-TYPE   8 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   30
  20P LOSS WILD-TYPE    8  295
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  8
  NOT HISPANIC OR LATINO               30                295
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    18  13
  20Q LOSS WILD-TYPE 248 277
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                31                525 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                13                277 
$`20Q LOSS MUTATED`
TCGA-04-1336 TCGA-09-1667 TCGA-09-2048 TCGA-13-0720 TCGA-13-0804 TCGA-13-0883 
       49.15        61.87         4.54        44.55        35.28        68.94 
TCGA-13-1489 TCGA-13-1494 TCGA-13-1495 TCGA-13-2059 TCGA-20-0987 TCGA-23-1028 
       82.88        38.20        49.25        12.23        23.05        49.41 
TCGA-23-1118 TCGA-23-1119 TCGA-23-2072 TCGA-24-1428 TCGA-24-1463 TCGA-24-1471 
       86.01       129.96        24.95        17.39        72.92         1.18 
TCGA-24-1552 TCGA-24-2030 TCGA-24-2298 TCGA-25-2392 TCGA-29-1695 TCGA-29-1702 
       41.39        53.95        53.26         1.02         0.79        18.67 
TCGA-29-1711 TCGA-29-1781 TCGA-36-1578 TCGA-61-1734 TCGA-61-2002 TCGA-61-2088 
       34.62         8.38        27.85        28.47        17.98         4.77 
TCGA-WR-A838 
        8.05 

$`20Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00         1.81         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
       11.87        65.52        63.09        48.76        21.57        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       65.46        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       71.47        82.39        56.55        41.59        19.99        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
      119.08        29.10        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       28.64        64.64        36.23        31.86        47.70        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       29.16         9.47        57.76        17.98        35.57         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 
       38.43        89.33        74.93        41.62        57.60        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       30.51        17.98         5.85         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 
        6.18         6.12        35.15       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       39.75        20.94        26.93        12.46        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       81.47        18.51        33.24        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       35.44        35.80        15.12        19.86         6.21        24.59 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       39.58         2.73        12.39        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       55.17         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       32.25        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       28.70        30.35        19.59         8.71         7.79         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 
        8.28         8.19        43.86        35.28        13.61       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       91.40        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       69.01        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       54.64        87.06        61.71        29.42        98.04        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 
       22.39        70.82        52.44        73.55         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       37.61        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.41         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       14.24         8.61        10.78         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
        8.42        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       19.10        16.70         2.93         2.66        47.54        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 
       40.54        15.39        26.83        31.76         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       18.90         2.24        51.35        54.51         3.22        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       68.68         4.57        33.30         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13         0.53       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       77.00        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       54.12        63.55        47.41         6.31         6.38         7.82 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
        7.99         7.86         0.76         6.25         6.02         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 
        5.36         4.83        28.37        19.17        18.67        43.53 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
        8.55        12.46        45.14       105.99         9.11         3.45 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
       22.22        26.96        57.40        64.27        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 
       41.06        51.91        58.09        88.50        70.62        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       19.53        44.09        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        3.48         3.72         3.81         4.37        11.28         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       81.11         4.87       152.02        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
      109.71        14.43        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
       70.45        44.61         0.82        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86         1.02        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
        2.99        12.00         2.96        18.58        18.02        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
        0.36        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       35.54        51.22        14.96        24.99        18.05        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       13.02        49.05        38.04         3.02        12.00        45.01 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       78.90        44.71        47.18       101.79        38.53        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32         0.53        16.90        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       41.98        29.23        17.00        85.68        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.12        31.23        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 
       12.36        11.84        12.30        14.93         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       34.62        86.17        65.00        62.47        45.11         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
       42.25        11.84        11.47         9.76        21.04        38.07 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       51.91        36.26         2.47        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
       44.91        34.78         6.12        36.62         1.22        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       24.26        30.05        48.79        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       22.49         6.71        42.51        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
       29.10        21.53        22.85        22.55         8.55        30.08 
TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       25.74        24.23        24.69        35.05        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.82        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       20.98        18.31        20.52        14.17         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       11.47         7.99        26.04        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
        7.46        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
        1.74        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       80.12        22.32       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
        5.42        44.81        20.52        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
       31.43        18.54        27.88         4.34        31.79        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       44.84        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        8.42         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
       31.30        37.05        42.51        48.92        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       43.43        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
        4.01        30.64        39.85        30.64         1.18        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
       45.40         4.80        51.72        71.74        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       60.62        65.52        55.50         6.48        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       44.52       125.75        22.22         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       39.68        18.94         0.79 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.79               0.26 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            129.96             180.20 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             34.62              27.88 
[1] "0.8 - 130.0 (34.6)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1.5"
D77V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  20Q LOSS MUTATED         0    31                0
  20Q LOSS WILD-TYPE       2   526                2
D77V3, multiclass
                  clus
vv                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  OMENTUM                         0                  2
  OVARY                          31                526
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V4, continuous
D77V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0  32
  20Q LOSS WILD-TYPE   3 536
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   32
  20Q LOSS WILD-TYPE    3  536
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 0                  3
  YES               32                536
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  20Q LOSS MUTATED    0  0  0  0
  20Q LOSS WILD-TYPE 14 26  5  3
D77V6, multiclass
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     1
  20Q LOSS WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q LOSS MUTATED                           2
  20Q LOSS WILD-TYPE                        30
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q LOSS MUTATED                                           0    28
  20Q LOSS WILD-TYPE                                         1   447
D77V7, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  3
  ASIAN                                                    1                 17
  BLACK OR AFRICAN AMERICAN                                2                 30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  1
  WHITE                                                   28                447
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1  20
  20Q LOSS WILD-TYPE   9 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   20
  20Q LOSS WILD-TYPE    9  305
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  9
  NOT HISPANIC OR LATINO               20                305
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    91 100
  21Q LOSS WILD-TYPE 175 190
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               191                365 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               100                190 
$`21Q LOSS MUTATED`
TCGA-04-1335 TCGA-04-1347 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 
        1.81        63.09        63.98        65.46        49.28        44.32 
TCGA-04-1365 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 
       76.57        55.43        48.89        28.64        36.23        31.86 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
       47.70        45.37        17.98        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1667 TCGA-09-1669 TCGA-09-1675 TCGA-09-2049 TCGA-09-2051 
       89.33        61.87        30.51        97.55       112.41        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0937 
       39.75        12.46        25.91        81.47        33.24        15.12 
TCGA-13-0723 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 
       39.58        15.19        17.82        55.17        11.38        11.54 
TCGA-13-0761 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 
       34.06        38.93        36.72        30.35         8.12        43.86 
TCGA-13-0883 TCGA-13-0886 TCGA-13-0887 TCGA-13-0891 TCGA-13-0899 TCGA-13-0900 
       68.94        74.27        66.67        69.01        56.15        57.07 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       47.84        44.94        44.84        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-1404 TCGA-13-1407 TCGA-13-1409 
       14.89        13.81         4.64         6.61         6.05         6.84 
TCGA-13-1411 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1494 
        4.21        29.42        98.04        22.39        70.82        38.20 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1501 TCGA-13-1507 TCGA-13-2061 TCGA-13-2065 
       49.25        54.31        32.84         4.77        10.78         8.75 
TCGA-20-1682 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1030 
       27.52        19.10         2.93         2.66        42.54        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1113 TCGA-23-1114 TCGA-23-1124 TCGA-23-2072 
       18.90         2.24        31.20        68.68        58.13        24.95 
TCGA-23-2077 TCGA-23-2641 TCGA-24-0968 TCGA-24-0975 TCGA-24-1103 TCGA-24-1105 
      115.89         2.76        19.66        21.80        54.12        47.41 
TCGA-24-1413 TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 TCGA-24-1431 TCGA-24-1434 
        6.31         7.99         0.76         5.95        19.17        18.67 
TCGA-24-1471 TCGA-24-1548 TCGA-24-1549 TCGA-24-1557 TCGA-24-1567 TCGA-24-1604 
        1.18        16.21        56.58        39.88        17.23        88.37 
TCGA-24-1614 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 
       48.33         4.37         5.79         5.52         9.80        30.21 
TCGA-24-1930 TCGA-24-2023 TCGA-24-2026 TCGA-24-2029 TCGA-24-2267 TCGA-24-2281 
       81.11        44.84        34.82        14.43        47.54        44.61 
TCGA-24-2288 TCGA-24-2298 TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 
        0.82        53.26        37.02        34.98        36.95        33.96 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       18.02         0.36         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2396 TCGA-29-1691 
       35.54        51.22        14.96        24.99         3.02        47.18 
TCGA-29-1695 TCGA-29-1699 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 
        0.79         0.53        18.25        34.62        17.00        66.81 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1784 TCGA-29-1785 
       22.98        24.36        17.33        12.36         5.36        34.62 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       86.17        65.00        62.47        21.04        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1866 TCGA-30-1891 
       36.26         2.47        15.68        48.10        36.62        30.05 
TCGA-30-1892 TCGA-31-1950 TCGA-31-1956 TCGA-36-1569 TCGA-36-1575 TCGA-36-1581 
       48.79        18.77        44.12        29.10         8.55        24.69 
TCGA-36-2530 TCGA-36-2538 TCGA-36-2545 TCGA-36-2548 TCGA-36-2552 TCGA-3P-A9WA 
       33.01        25.08        18.31        14.17        11.47         7.99 
TCGA-42-2587 TCGA-42-2593 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2372 
       23.74         1.48        25.08        25.02       180.20        44.81 
TCGA-59-A5PD TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       20.52        18.54        27.88         4.34        31.79        28.47 
TCGA-61-1741 TCGA-61-1899 TCGA-61-1904 TCGA-61-1913 TCGA-61-1918 TCGA-61-1919 
       33.67         8.42         9.07        48.92        15.75        38.17 
TCGA-61-2008 TCGA-61-2016 TCGA-61-2094 TCGA-61-2113 TCGA-WR-A838 
       30.64         1.18        71.74        22.22         8.05 

$`21Q LOSS WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1361 TCGA-04-1364 
       11.87        65.52        48.76        21.57        32.52        33.67 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       71.47        82.39        56.55        41.59        19.99        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-09-0364 
      119.08        29.10        84.20        27.88        64.64        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 
        9.47        57.76        74.93        41.62        57.60        55.36 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 
       17.98         5.85         3.02         8.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-10-0925 
       35.15         4.54        71.11        20.94        26.93        54.31 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       18.51        32.28        11.70         3.91        35.44        35.80 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 
       19.86         6.21        24.59        44.55         2.73        12.39 
TCGA-13-0726 TCGA-13-0755 TCGA-13-0757 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
       31.10         2.50        11.18        32.25        31.04        21.40 
TCGA-13-0768 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
        8.45        28.70        19.59         8.71         7.79         8.28 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 
        8.19        35.28        35.28        13.61       107.18        91.40 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 
       70.39        61.84        67.99        43.36        57.47        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0910 TCGA-13-0911 TCGA-13-0923 TCGA-13-0924 
       47.38        48.33        37.08        27.72         6.41         6.08 
TCGA-13-1403 TCGA-13-1405 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
       10.88         7.36         5.92         4.70         5.33        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       87.06        61.71        20.68        82.88        52.44        73.55 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 
        4.24        37.61        38.40        13.97        16.57         4.21 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
        4.41         4.18         2.56         3.91         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       12.23         8.61         6.28        54.77         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1685 TCGA-23-1021 
       25.94        26.20        72.20        25.38        16.70        47.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        31.76        49.41         8.81 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       51.35        54.51         3.22         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 
      129.96         4.27         6.38        39.09        33.47         0.53 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 
       87.48        91.66        77.00        49.84         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 
        7.63        11.64        41.56         7.66        22.32        63.55 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 
        6.38         7.82         7.86         6.25         6.02         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
        4.83        17.39        28.37        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 
       12.46        45.14       105.99         9.11         3.45        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       26.96        57.40        64.27        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       58.09        88.50        70.62        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1616 TCGA-24-1842 
       47.70        25.87        10.26        90.15        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1923 TCGA-24-1927 
        3.48         3.72         3.81        11.28        22.68        16.44 
TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2027 TCGA-24-2030 
       11.05         4.87       152.02        58.16       109.71        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 
       18.48        28.18        64.01        44.52        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2289 TCGA-24-2290 
        0.79         0.36        31.63        70.45        67.36        36.23 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       16.64        33.11        55.86         1.02        26.96        32.02 
TCGA-25-1315 TCGA-25-1317 TCGA-25-1319 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       51.06         1.02        65.00         2.99        12.00         2.96 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       18.58        15.81        20.61        18.05        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       49.05         1.02        38.04        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       42.02         2.96        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
       44.71       101.79        38.53        33.70        31.20        68.32 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1762 
       16.90        18.67        59.67        41.98        29.23        85.68 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 
       62.93        39.12        31.23        22.55        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 
       14.93         8.38         7.23        45.11         4.90        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 
       11.84        11.47         9.76         0.26        44.91        34.78 
TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-31-1944 TCGA-31-1946 
        6.12         1.22        57.57        24.26        45.57        30.18 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 
       22.49         6.71        42.51         2.20        28.77        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.85        22.55        30.08        25.74        27.85        24.23 
TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 
       35.05        29.49        29.82        25.91        23.80        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 
        2.24        20.98        20.52         6.05        16.18        26.04 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
        9.44        42.02         7.46        40.77        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-59-2349 TCGA-59-2350 
       21.14         1.74        22.32        29.00        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 
      116.12         9.40        34.39         2.14         5.42        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
        8.09        20.94        31.43        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
        2.43        43.69         1.45         5.79        11.41        13.02 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 
       34.13        31.30        37.05        42.51        56.61        67.76 
TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 
       43.43         2.01         5.52        14.50        17.98         4.01 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       39.85        30.64        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       51.72        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2612 
        6.48        76.87        20.68        44.52       125.75         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       31.07         8.61        39.68        18.94         0.79 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.30               0.26 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            180.20             152.02 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             30.05              26.93 
[1] "0.3 - 180.2 (30.1)" "0.3 - 152.0 (26.9)"
[1] "hr=" "1"  
D78V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  21Q LOSS MUTATED         0   191                0
  21Q LOSS WILD-TYPE       2   366                2
D78V3, multiclass
                  clus
vv                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  OMENTUM                         0                  2
  OVARY                         191                366
  PERITONEUM OVARY                0                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V4, continuous
D78V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1 193
  21Q LOSS WILD-TYPE   2 375
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1  193
  21Q LOSS WILD-TYPE    2  375
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 1                  2
  YES              193                375
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED    4  8  1  1
  21Q LOSS WILD-TYPE 10 18  4  2
D78V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0                4                 10
  R1                8                 18
  R2                1                  4
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     3
  21Q LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q LOSS MUTATED                          11
  21Q LOSS WILD-TYPE                        21
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           1   166
  21Q LOSS WILD-TYPE                                         0   309
D78V7, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  2
  ASIAN                                                    3                 15
  BLACK OR AFRICAN AMERICAN                               11                 21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  166                309
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     3 119
  21Q LOSS WILD-TYPE   7 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3  119
  21Q LOSS WILD-TYPE    7  206
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  7
  NOT HISPANIC OR LATINO              119                206
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   192 224
  22Q LOSS WILD-TYPE  74  66
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               416                140 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               224                 66 
$`22Q LOSS MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1346 
       40.24        49.15         2.01        46.62        18.51        65.52 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       63.09        21.57        63.98        65.46        49.28        32.52 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       44.32        76.57        71.47        82.39        56.55        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       38.37       119.08        84.20        55.43        48.89        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
        9.47        57.76        17.98        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       89.33        74.93        57.60        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2048 
       17.98         3.02         8.55        97.55         6.12         4.54 
TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 
      112.41        71.11        63.09        39.75        20.94        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 
       54.31        25.91        81.47        18.51        32.28        11.70 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       15.12        19.86         6.21        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
        2.73        12.39        15.19        17.82        55.17        11.18 
TCGA-13-0758 TCGA-13-0761 TCGA-13-0766 TCGA-13-0791 TCGA-13-0794 TCGA-13-0795 
       11.38        34.06        21.40        38.93        30.35        19.59 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        7.79         8.12         8.28         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 
       66.67        70.39        61.84        67.99        69.01        57.47 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 
       57.07        19.36        47.38        48.33        44.94        44.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       37.08        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 
        4.64         6.41         6.08         6.61         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 
        6.84         4.70         4.21         5.33        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       29.42        98.04        22.39        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       38.20        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       13.97        16.57         4.21         4.41         4.77         4.18 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        3.09        14.24        12.23         8.61        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
        6.28        54.77         8.42        25.94        26.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
       25.38        19.10        16.70         2.66        47.54        42.54 
TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       15.39        31.76        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        2.24        51.35        54.51        31.20        68.68         4.57 
TCGA-23-1117 TCGA-23-1122 TCGA-23-1123 TCGA-23-2072 TCGA-23-2078 TCGA-23-2081 
       33.30        39.09        33.47        24.95        87.48        77.00 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 
       49.84         2.76         4.70         4.50         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 
       11.64        21.80        41.56        22.32        63.55        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
        6.31         6.38         7.82         7.99         7.86         0.76 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        6.25         6.02         5.95         5.36         4.83        17.39 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 
       19.17        18.67        43.53         8.55        12.46        45.14 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 
        1.18        22.22        26.96        57.40        16.21        56.58 
TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 
       41.06        41.39        88.50        39.88        44.09        45.50 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       25.87        10.26        17.23        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1850 
       38.24         8.32         3.48         3.72         4.37         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
        9.80        22.68        30.21        81.11         4.87       152.02 
TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       44.84        34.82       109.71        14.43        53.95        18.48 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       64.01        57.07        36.16         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 
       31.63        70.45         0.82        16.64        33.11        53.26 
TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
        1.02        32.02        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
       65.00        36.95        33.96         2.99         2.96        18.58 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       15.81        20.61         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       51.22        14.96        24.99        18.05        85.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 
       49.05         1.02        38.04        12.00        45.01        19.99 
TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1693 TCGA-29-1694 
       42.02        29.03        31.00        26.99       101.79        38.53 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 
        0.79        33.70        31.20        68.32        16.90        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 
       59.67        18.25        41.98        34.62        17.00        66.81 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 
       39.12        22.98        17.33        12.36        11.84        14.93 
TCGA-29-1783 TCGA-29-1785 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-A5NZ 
        7.23        34.62        45.11         4.90        11.84        21.04 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
       38.07        51.91        36.26         2.47        15.68        48.10 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       44.91         6.12        36.62         1.22        57.57        24.26 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       48.79        45.57        22.49         6.71        42.51         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       28.77        29.10        22.85         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       27.85        24.23        24.69        33.01        29.49        29.82 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2548 
       25.08        23.80        21.60         2.24        20.98        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       16.18        11.47         7.99         9.44        42.02         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1992 
       40.77         1.48        24.03        11.38        21.14        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       25.08        25.02       180.20        22.32       116.12         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 
       34.39         2.14         5.42        44.81         8.09        31.43 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 
       27.88         4.34        31.79        48.79        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 
       33.67        43.69         8.42         5.79        11.41        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       31.30        37.05        48.92        67.76        43.43        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 
       38.17         2.01         5.52        14.50         4.01        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2096 
       30.64         1.18        45.40         4.80         4.77        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       60.62        65.52         6.48        20.68        44.52       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
       22.22         6.35        31.07         8.61        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

$`22Q LOSS WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1343 TCGA-04-1348 TCGA-04-1364 TCGA-04-1516 
       41.00         1.81        11.87        48.76        33.67        41.59 
TCGA-04-1536 TCGA-04-1654 TCGA-09-1665 TCGA-09-1672 TCGA-09-2043 TCGA-09-2045 
       29.10        47.70        41.62         5.85         6.18        35.15 
TCGA-09-2055 TCGA-10-0930 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0726 
       26.93        33.24         3.91        35.44        35.80        31.10 
TCGA-13-0755 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0792 
        2.50        11.54        32.25        31.04         8.45        36.72 
TCGA-13-0793 TCGA-13-0797 TCGA-13-0893 TCGA-13-0899 TCGA-13-0905 TCGA-13-0920 
       28.70         8.71        43.36        56.15        47.84        13.81 
TCGA-13-1403 TCGA-13-1405 TCGA-13-1477 TCGA-13-1485 TCGA-13-1488 TCGA-13-1501 
       10.88         7.36        54.64        20.68        70.82        32.84 
TCGA-13-1510 TCGA-13-1511 TCGA-20-0987 TCGA-20-0996 TCGA-20-1686 TCGA-23-1023 
        2.56         3.91        23.05        72.20         2.93        40.54 
TCGA-23-1026 TCGA-23-1111 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       26.83         3.22        86.01       129.96         4.27         6.38 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 TCGA-24-0980 TCGA-24-1103 
       58.13         0.53       115.89        91.66         7.66        54.12 
TCGA-24-1430 TCGA-24-1463 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1546 
       28.37        72.92       105.99         9.11         3.45        64.27 
TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1558 TCGA-24-1563 TCGA-24-1845 
       51.91        58.09        70.62        19.53        47.70         3.81 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1927 TCGA-24-1928 TCGA-24-2024 TCGA-24-2035 
       11.28         5.79        16.44        11.05        58.16        28.18 
TCGA-24-2038 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-25-1313 
       44.52        44.61        67.36        36.23        55.86        26.96 
TCGA-25-1323 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-2396 TCGA-25-2401 
       12.00        18.02         0.36         7.86         3.02         2.96 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1699 TCGA-29-1710 TCGA-29-1762 
       78.90        44.71        47.18         0.53        29.23        85.68 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1777 TCGA-29-1781 
       62.93        31.23        24.36        22.55        12.30         8.38 
TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2434 
        5.36        86.17        65.00        62.47        42.25        11.47 
TCGA-29-2436 TCGA-30-1857 TCGA-30-1861 TCGA-30-1891 TCGA-31-1946 TCGA-31-1950 
        9.76         0.26        34.78        30.05        30.18        18.77 
TCGA-31-1956 TCGA-36-1570 TCGA-36-1574 TCGA-36-2529 TCGA-36-2537 TCGA-36-2545 
       44.12        21.53        22.55        35.05        25.91        18.31 
TCGA-36-2547 TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 TCGA-57-1585 TCGA-57-1586 
       20.52         6.05        26.04        23.74         1.74        22.32 
TCGA-59-2349 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1727 TCGA-61-1734 
       80.12        20.52        11.11        20.94        18.54        28.47 
TCGA-61-1737 TCGA-61-1895 TCGA-61-1903 TCGA-61-1904 TCGA-61-1911 TCGA-61-1914 
       44.84         1.45        13.02         9.07        42.51        56.61 
TCGA-61-2002 TCGA-61-2008 TCGA-61-2017 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       17.98        30.64        45.96        51.72        71.74        61.64 
TCGA-61-2101 TCGA-61-2104 
       55.50        76.87 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.30               0.26 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            180.20             129.96 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            27.785             28.585 
[1] "0.3 - 180.2 (27.8)" "0.3 - 130.0 (28.6)"
[1] "hr=" "1.2"
D79V2, continuous
                    vv
clus                 OMENTUM OVARY PERITONEUM OVARY
  22Q LOSS MUTATED         1   417                1
  22Q LOSS WILD-TYPE       1   140                1
D79V3, multiclass
                  clus
vv                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  OMENTUM                         1                  1
  OVARY                         417                140
  PERITONEUM OVARY                1                  1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V4, continuous
D79V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3 424
  22Q LOSS WILD-TYPE   0 144
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3  424
  22Q LOSS WILD-TYPE    0  144
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 3                  0
  YES              424                144
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED    6 20  5  3
  22Q LOSS WILD-TYPE  8  6  0  0
D79V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0                6                  8
  R1               20                  6
  R2                5                  0
  RX                3                  0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  3    14
  22Q LOSS WILD-TYPE                                0     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q LOSS MUTATED                          24
  22Q LOSS WILD-TYPE                         8
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           1   356
  22Q LOSS WILD-TYPE                                         0   119
D79V7, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         3                  0
  ASIAN                                                   14                  4
  BLACK OR AFRICAN AMERICAN                               24                  8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  0
  WHITE                                                  356                119
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     8 248
  22Q LOSS WILD-TYPE   2  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      8  248
  22Q LOSS WILD-TYPE    2   77
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  2
  NOT HISPANIC OR LATINO              248                 77
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED   122 142
  XQ LOSS WILD-TYPE 144 148
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              264               292 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              142               148 
$`XQ LOSS MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 
       40.24        41.00        49.15        11.87        63.09        48.76 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       32.52        44.32        33.67        76.57        71.47        56.55 
TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       19.99       119.08        29.10        55.43        48.89        28.64 
TCGA-04-1651 TCGA-04-1654 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       36.23        47.70        57.76        17.98        35.57         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1673 
       38.43        89.33        74.93        57.60        61.87         3.02 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       97.55         6.12       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 
       20.94        26.93        12.46        54.31        25.91        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0725 
       33.24        32.28        15.12        19.86         6.21        12.39 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0799 
       11.38        11.54        21.40        38.93        36.72         7.79 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0887 
        8.28        43.86        35.28        13.61        68.94        66.67 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
       61.84        69.01        57.07        47.38        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 
       44.84        37.08        29.98        14.89        13.81         6.08 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 
        7.36         6.05         5.92         5.33        61.71        29.42 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 
       22.39        82.88        52.44        73.55        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       54.31        37.61        13.97         4.77         4.18         2.56 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
        3.09        12.23        10.78        27.52        25.38        19.10 
TCGA-23-1022 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       42.54        31.76        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1113 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-2079 
        2.24        31.20         4.27        39.09        33.47        91.66 
TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 TCGA-24-0980 TCGA-24-1103 
       77.00         2.76         7.63        11.64         7.66        54.12 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 
       47.41         6.31         6.38         7.82         7.86         6.25 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        5.95         5.36         4.83        17.39        28.37        19.17 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 
       43.53        72.92        12.46        45.14         9.11         3.45 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 
       64.27        16.21        56.58        41.06        41.39        88.50 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1845 
       44.09        45.50        17.23        90.15        48.33         3.81 
TCGA-24-1849 TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 
        5.79        81.11        44.84        58.16       109.71        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 
       53.95        18.48        28.18        64.01        57.07        36.16 
TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 
        0.36        31.63        70.45         0.82        67.36        36.23 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1322 
       55.86        53.26        32.02        51.06        37.02         2.99 
TCGA-25-1625 TCGA-25-1630 TCGA-25-1631 TCGA-25-1635 TCGA-25-1870 TCGA-25-1878 
       18.02         7.86         0.30        51.22        14.96        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2399 TCGA-25-2409 
       13.02        49.05         1.02         3.02        19.99        26.99 
TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1702 
       78.90       101.79        38.53        33.70        31.20        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       59.67        18.25        41.98        34.62        17.00        85.68 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 
       22.98        22.55        12.36        12.30         8.38         5.36 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 TCGA-30-1853 
       86.17        62.47        42.25        11.84        38.07        36.26 
TCGA-30-1857 TCGA-30-1866 TCGA-30-1880 TCGA-30-1891 TCGA-31-1944 TCGA-31-1953 
        0.26        36.62        57.57        30.05        45.57         6.71 
TCGA-31-1955 TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 
       42.51        44.12        29.10        21.53        22.55         8.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       25.74        27.85        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 TCGA-3P-A9WA TCGA-42-2582 
       25.08        21.60        18.31        20.52         7.99        26.04 
TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 
       42.02        40.77         1.48         1.74        29.00        25.08 
TCGA-57-1994 TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1724 
       25.02        22.32        34.39         5.42        20.52        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1743 
       31.43        18.54        48.79        44.84        35.80        43.69 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1913 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       11.41        13.02        48.92        15.75        38.17         2.01 
TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2088 
       17.98        30.64        30.64         1.18        45.40         4.77 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2104 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 
       58.39        65.52        76.87        44.52        22.22        31.07 

$`XQ LOSS WILD-TYPE`
TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1346 TCGA-04-1349 
        1.81         2.01        46.62        18.51        65.52        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 
       63.98        65.46        49.28        82.39        41.59        38.37 
TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       84.20        27.88        64.64        31.86        45.37        29.16 
TCGA-09-0365 TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
        9.47        41.62        55.36        30.51        17.98         5.85 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-10-0927 TCGA-10-0933 
        8.55         6.18        35.15         4.54        81.47        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
        3.91        35.44        35.80        24.59        44.55        39.58 
TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
        2.73        31.10        15.19        17.82        55.17         2.50 
TCGA-13-0757 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0793 
       11.18        34.06        32.25        31.04         8.45        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 
       30.35        19.59         8.71         8.12         8.19        35.28 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 
      107.18        91.40        74.27        70.39        67.99        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0911 TCGA-13-0912 
       57.47        56.15        19.36        48.33        27.72        34.06 
TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 TCGA-13-1404 TCGA-13-1409 
       21.17         4.64         6.41        10.88         6.61         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 
        4.70         4.21        54.64        87.06        98.04        20.68 
TCGA-13-1488 TCGA-13-1494 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       70.82        38.20        38.40        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 
        4.41         3.91        14.24         8.61         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       54.77         8.42        23.05        25.94        26.20        72.20 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 
       16.70         2.93         2.66        47.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 
       26.83        51.35        54.51         3.22        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 
       33.30        86.01       129.96         6.38        58.13         0.53 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 
       24.95       115.89        87.48        49.84         4.70         4.50 
TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1418 
       19.66        21.80        41.56        22.32        63.55         7.99 
TCGA-24-1422 TCGA-24-1424 TCGA-24-1434 TCGA-24-1436 TCGA-24-1467 TCGA-24-1471 
        0.76         6.02        18.67         8.55       105.99         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 
       22.22        26.96        57.40        51.91        58.09        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1604 
       39.88        19.53        47.70        25.87        10.26        88.37 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 
       38.24         8.32         3.48         3.72         4.37        11.28 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        5.52         9.80        22.68        30.21        16.44        11.05 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 TCGA-24-2038 TCGA-24-2261 TCGA-24-2267 
        4.87       152.02        34.82        44.52         0.79        47.54 
TCGA-24-2281 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 TCGA-25-1317 
       44.61        16.64        33.11         1.02        26.96         1.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 
       34.98        65.00        36.95        33.96        12.00         2.96 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1632 TCGA-25-1633 
       18.58        15.81         0.36        20.61        56.94        60.59 
TCGA-25-1634 TCGA-25-1871 TCGA-25-1877 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 
       35.54        24.99        18.05        38.04        12.00        45.01 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 
       42.02         2.96        29.03        31.00        44.71        47.18 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1710 TCGA-29-1763 
        0.79        68.32         0.53        16.90        29.23        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1776 
       62.93        39.12        31.23        24.36        17.33        11.84 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 
       14.93         7.23        34.62        65.00        45.11         4.90 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
       11.47         9.76        21.04        51.91         2.47        15.68 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 
       48.10        44.91        34.78         6.12         1.22        24.26 
TCGA-30-1892 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1959 TCGA-36-1568 
       48.79        30.18        18.77        22.49         2.20        28.77 
TCGA-36-1571 TCGA-36-1576 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2540 
       22.85        30.08        24.23        24.69        35.05        23.80 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 
        2.24        20.98        14.17         6.05        16.18        11.47 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       23.74         9.44         7.46        24.03        11.38        21.14 
TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 
       22.32       180.20        80.12       116.12         9.40         2.14 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 
       44.81        11.11         8.09        27.88         4.34        31.79 
TCGA-61-1734 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       28.47         2.43        33.67         1.45         8.42         5.79 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 
        9.07        34.13        31.30        37.05        42.51        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 
       67.76        43.43         5.52        14.50         4.01        39.85 
TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
       45.96         4.80        51.72        71.74        61.64        60.62 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 
       55.50         6.48        20.68       125.75         6.35         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       39.68        18.94         0.79         8.05 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.26              0.36 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           119.08            180.20 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           30.345            24.640 
[1] "0.3 - 119.1 (30.3)" "0.4 - 180.2 (24.6)"
[1] "hr=" "1"  
D80V2, continuous
                   vv
clus                OMENTUM OVARY PERITONEUM OVARY
  XQ LOSS MUTATED         1   265                0
  XQ LOSS WILD-TYPE       1   292                2
D80V3, multiclass
                  clus
vv                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  OMENTUM                        1                 1
  OVARY                        265               292
  PERITONEUM OVARY               0                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V4, continuous
D80V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3 271
  XQ LOSS WILD-TYPE   0 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3  271
  XQ LOSS WILD-TYPE    0  297
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                3                 0
  YES             271               297
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  XQ LOSS MUTATED    8 12  1  1
  XQ LOSS WILD-TYPE  6 14  4  2
D80V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0               8                 6
  R1              12                14
  R2               1                 4
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  2    13
  XQ LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ LOSS MUTATED                          13
  XQ LOSS WILD-TYPE                        19
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           1   225
  XQ LOSS WILD-TYPE                                         0   250
D80V7, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        2                 1
  ASIAN                                                  13                 5
  BLACK OR AFRICAN AMERICAN                              13                19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 0
  WHITE                                                 225               250
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     4 151
  XQ LOSS WILD-TYPE   6 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4  151
  XQ LOSS WILD-TYPE    6  174
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 6
  NOT HISPANIC OR LATINO             151               174
[1] 2 2
[1] FALSE
