[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"        "-oTUCEC-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/UCEC-TP/10006384/UCEC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/10013833/transformed.cor.cli.txt"

nPatients in clinical file=497, in cluster file=524, common to both=485
[1]  80 485
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               40               445 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               40               445 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              165               320 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              165               320 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               83               402 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               83               402 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               67               418 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               67               418 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               38               447 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               38               447 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               67               418 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               67               418 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               473 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               473 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               477 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               477 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               47               438 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               47               438 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               18               467 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               18               467 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               69               416 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               69               416 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               56               429 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               56               429 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               58               427 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               58               427 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               56               429 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               56               429 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              107               378 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              107               378 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              139               346 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              139               346 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               18               467 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               18               467 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7               478 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7               478 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               108                377 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               108                377 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               102                383 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               102                383 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                19                466 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                19                466 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                468 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                468 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                59                426 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                59                426 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                46                439 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                46                439 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                27                458 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                27                458 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                449 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                449 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                476 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                476 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                462 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                462 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 9                476 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 9                476 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                11                474 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                11                474 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                25                460 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                25                460 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                62                423 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                62                423 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                38                447 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                38                447 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                45                440 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                45                440 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                47                438 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                47                438 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                97                388 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                97                388 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               113                372 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               113                372 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                32                453 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                32                453 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                29                456 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                29                456 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               58               427 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               58               427 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               464 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               464 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13               472 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13               472 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               475 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               475 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               469 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               469 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               46               439 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               46               439 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               29               456 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               29               456 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               86               399 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               86               399 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               86               399 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               86               399 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               48               437 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               48               437 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               66               419 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               66               419 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               15               470 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               15               470 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22               463 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22               463 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               39               446 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               39               446 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               37               448 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               37               448 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               69               416 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               69               416 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               464 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               464 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               89               396 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               89               396 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              106               379 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              106               379 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                34                451 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                34                451 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                33                452 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                33                452 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                65                420 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                65                420 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                62                423 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                62                423 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                39                446 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                39                446 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                454 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                454 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                76                409 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                76                409 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                53                432 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                53                432 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                94                391 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                94                391 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                84                401 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                84                401 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               122                363 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               122                363 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               109                376 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               109                376 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                79                406 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                79                406 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                44                441 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                44                441 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                55                430 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                55                430 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                53                432 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                53                432 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                50                435 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                50                435 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                16                469 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                16                469 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                477 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                477 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                48                437 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                48                437 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                94                391 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                94                391 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               64               421 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               64               421 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 485 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
          NA         4549         1126         2540           NA          997 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
          98         3205         2656         2254         1750         2000 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
        1841         1841         1416         1167         1120          860 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
         633          706         2088          607          535          596 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
         749          884         1288          485          241          348 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
        1105          292          244         2769         1409           NA 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
         162          157          223          455           36           33 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
          60           12          602           26           73           92 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BH TCGA-AJ-A3BI TCGA-AJ-A3BK 
          15           34           23           NA           68           51 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
          NA          446          684          677           39           28 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
        1125          628           41          475           23           59 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 
         485           57          513           52           71         2545 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
          NA          181           NA         2618          250         1199 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        1758         1385         1122          239          371          636 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
          NA         3815         3589         3357          103         1921 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
          NA         2972          965         2554          825         2510 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
          NA         1875         2457         1918         1497          763 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
        2180         1836         1700          952           NA         1276 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
        1495          204          940          317          847          494 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
         555         1026           17           NA          603          903 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
        2079         2191         1413         1075         1399         2025 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
        1064         1640           NA         1554          833          913 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
        1845         1065          868         1149         1333         1220 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
        2004          404          584          516          412          464 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
         617          378          610         2337         2207         1646 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
        2053          764         1107          337           NA           NA 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
        2167         1020         1861         2090         1016         1232 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
         589          801          540          831           NA           NA 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
        1177            7            3           10            4            6 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
          NA            1            4           NA            7           36 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
         254          440            4         2445         1731         1422 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
        1312         1483         1237         1360          990          871 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
         862          928          788          700          544          418 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
         520          543          335          125          265         5651 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
        3448         2687         2303         1656         1396         1337 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
        1232         1120          976         1019          832          509 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
         595          593          560          528          504         5835 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
          NA           NA          438          447          356           NA 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
         465          389         1890          153         1249         1038 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
        1063          566          614          588          637         1071 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
        1064          241         1167         1110          860           NA 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
        1263         1477           NA           NA         1309         1196 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
         937          644          617          469          742          811 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
         497         1043          868         1607         1721          451 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
         382          419          448          426          470          470 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
         434           55          291         1085          721          612 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
         344          207         1092         1064          189          311 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
         309          966          760          734          506          401 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
         305          300           NA          714         2602         2379 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
          NA         2371         1882         2068         2935           NA 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
        2963         2044         2687         2611         2506         2481 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
        2212         2228         1810         1910         1934         1507 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
        1921         2022          512          602          911          260 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
          17          148          872          728          686           53 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
         135          669         1201          915          909           NA 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
         112          892          991           20          478         1098 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
        1135         1106         1141         1119           NA           NA 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
         910          945         1023          324           21          568 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
          43          111          532          594          202          917 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
         548          206           48          213           30          926 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
          39          852          854          802          311           46 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
          54           NA          739           71          697           43 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
         402           22          555          513          548           63 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
         458           32           NA          107         1260           NA 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU 
        1365            8          130          125          496         1195 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
        1114          739         1076           NA           NA           NA 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
        2797          711         1471          519           NA          203 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
         487          224          511          332          243          328 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
         972         1066         1004          825          982          754 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
         985           NA         1046          589         1069          392 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
         826          820          677          497           NA           NA 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
         138          248          741          826          710          710 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
         727          693          425          210          586          573 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
         544          536          459          490          378          481 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
         260          197          588          383          110          438 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
         574          694          409         1392          944          885 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
         832          421          196          545           65          212 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
         113          161         1217         1064         1034         1095 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
          NA           NA          273         2941         1795          276 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
          NA          881          761          791           NA           53 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
         400           74          329          128          168 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=397,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=27,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "COMPLETENESS.OF.RESECTION"             
[5] "RACE"                                  
[6] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 485 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=58, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
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    31   9
  1P GAIN WILD-TYPE 392  51
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               40               443 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                9                51 
$`1P GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GA TCGA-A5-A1OG TCGA-A5-A1OK TCGA-A5-A3LP TCGA-AJ-A3BD 
       37.02        17.85        11.44         8.02        14.96         0.49 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AP-A052 TCGA-AP-A3K1 TCGA-AP-A5FX 
        0.92         0.76        16.87        21.99        18.25        33.73 
TCGA-AX-A0IW TCGA-AX-A1CI TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
       37.78        72.56         0.13        20.52         0.03         0.13 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C TCGA-BG-A222 TCGA-BK-A139 TCGA-BK-A4ZD 
        5.03        34.13        15.45         9.57        10.16        16.64 
TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A177 TCGA-D1-A17R 
       61.87        67.20        11.51        18.67        18.02        11.15 
TCGA-DI-A1NO TCGA-E6-A2P9 TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EY-A212 TCGA-EY-A2ON 
        9.37         6.67        34.39        22.26         3.62        13.45 
TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-KJ-A3U4 
        3.72        36.00        59.01         2.43 

$`1P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
      106.88       149.56        83.51        32.78         3.22       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
       87.32        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 
       42.35        15.95         7.92        36.33         9.60        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M 
       46.32        28.64         5.33         5.16         7.33         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.08         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        3.02         1.12         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26         1.28        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW 
        1.35        15.62         1.94        15.95         1.87         1.71 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        2.33        83.67         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       39.42        57.80        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        28.54        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        76.83        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.33         0.20         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.13        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        14.27         1.81        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31         6.81        35.90        34.98         6.21        10.22 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        24.13        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27         4.11        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
       35.38        12.39        31.10        91.96        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
       17.06         2.37        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV 
       32.28        24.79        32.38        19.40        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        26.96        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 
        8.55         6.48        19.33        12.59        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        45.76        31.04        29.10        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX 
        6.44        17.92         2.14         6.97         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       34.98        33.99         7.99        13.84         8.98        96.69 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
        9.07        28.93        28.96        25.02        26.01        41.06 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74        13.15        10.82         4.21         5.52 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.03              0.10 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            72.56            191.84 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           15.205            23.700 
[1] "0.0 - 72.6 (15.2)"  "0.1 - 191.8 (23.7)"
[1] "hr=" "2.8"
D1V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1P GAIN MUTATED                                        17
  1P GAIN WILD-TYPE                                     350
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1P GAIN MUTATED                               2
  1P GAIN WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1P GAIN MUTATED                                  21
  1P GAIN WILD-TYPE                                77
D1V3, multiclass
                                         clus
vv                                        1P GAIN MUTATED 1P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              17               350
  MIXED SEROUS AND ENDOMETRIOID                         2                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    21                77
[1] 3 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, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     6  34
  1P GAIN WILD-TYPE 132 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6   34
  1P GAIN WILD-TYPE  132  313
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                6               132
  YES              34               313
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    24   0   2   6
  1P GAIN WILD-TYPE 312  22  15  23
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              24               312
  R1               0                22
  R2               2                15
  RX               6                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     1
  1P GAIN WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P GAIN MUTATED                          10
  1P GAIN WILD-TYPE                        63
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P GAIN MUTATED                                           2    25
  1P GAIN WILD-TYPE                                         7   330
D1V6, multiclass
                                           clus
vv                                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                              10                63
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  25               330
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  30
  1P GAIN WILD-TYPE  12 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   30
  1P GAIN WILD-TYPE   12  306
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              30               306
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   139  25
  1Q GAIN WILD-TYPE 284  35
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              164               319 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               25                35 
$`1Q GAIN MUTATED`
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GG TCGA-A5-A0GI TCGA-A5-A0GN 
       83.51        17.85        32.78        87.32        57.53        60.53 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       28.27        20.81        68.65        11.44        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A3BD TCGA-AJ-A3EJ 
        8.02        46.32        14.96         1.97         0.49         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3OL 
       22.26         0.92        36.99         1.35         0.76         1.87 
TCGA-AJ-A3QS TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05P TCGA-AP-A0LD 
       16.87        83.67        21.99        23.31        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A1DM TCGA-AP-A1DO 
      110.37        36.36        97.71        83.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1E1 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S 
       35.54        10.42        16.24        18.25        33.73        13.58 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 
       68.35        72.03        46.45        35.34        66.58        34.98 
TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CI 
       35.01        37.78        65.88        13.55        20.28        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A3FX 
       54.12        67.50        68.71        17.75        31.13         0.13 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3GB TCGA-AX-A3GI 
       20.52         0.03         0.13         1.18        14.47         0.13 
TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A0K6 
       56.91        43.13        40.67        28.34        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       17.10        11.01        36.82        32.09        33.50        27.35 
TCGA-B5-A11Z TCGA-B5-A1MU TCGA-B5-A1MZ TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LX 
       17.36        50.89        15.29         5.03        41.06        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0MO 
       19.33        20.94        35.21        34.98         7.92        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0W1 TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A3EW 
       52.83        13.78        15.45         1.81         9.57        11.31 
TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U7 
       35.90        10.16        31.76        24.13        61.87        30.74 
TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       67.20        72.72        59.51        63.16        16.83         8.55 
TCGA-D1-A0ZR TCGA-D1-A102 TCGA-D1-A160 TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16S 
        0.56         4.44         3.68         0.66        11.51        18.67 
TCGA-D1-A16V TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17L 
        1.41        30.15        18.02         1.58         7.00        26.37 
TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A2G5 TCGA-D1-A2G6 
       10.22        11.15        16.87        18.02        41.42         8.48 
TCGA-D1-A3DA TCGA-DI-A0WH TCGA-DI-A1NO TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EO-A22Y 
        0.26        16.31         9.37         6.67         7.36        24.79 
TCGA-EO-A3AS TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GF TCGA-EY-A1GK 
       34.39         6.21         4.54         8.15        27.16        22.78 
TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX 
       19.27        17.88        15.09        16.11        12.43         6.48 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR 
        3.62        14.40        13.45        45.76        31.04         6.44 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2F4 
        6.97         3.72         5.29        36.00        59.01        28.96 
TCGA-FI-A3PV TCGA-KJ-A3U4 
       41.06         2.43 

$`1Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
      106.88       149.56        37.02         3.22       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GW 
       65.75        60.53        46.55        38.37        36.82        23.21 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       15.95         7.92        91.04        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        7.33         1.18         1.08         0.39        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40         3.02         1.12         0.76         2.24         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       14.66        22.49         1.28        20.65        15.62         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A053 TCGA-AP-A056 TCGA-AP-A059 
       15.95         1.71         2.33         5.95        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       39.42        57.80        45.53        36.89         7.86        12.20 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LM 
       48.79       125.42         3.39        63.16        31.73        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       25.08        71.67        60.36        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E3 TCGA-AW-A1PO TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A062 
       30.90        27.85         0.56        19.82        29.69        45.99 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       28.54        43.82        40.11        13.28        19.20        16.96 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CN TCGA-AX-A1CP 
       15.25        12.43        20.05        76.83        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        33.53        61.18 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       33.40        40.50        19.36        26.33        27.32         2.96 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 
       38.70         0.23         0.10         0.33         0.20         0.23 
TCGA-AX-A3G9 TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0JY 
        8.35        80.38        46.75        48.76        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB 
       28.64        30.51        25.91        23.01        17.85         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       45.90        43.96        40.50        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW 
       18.41        16.57       191.84       102.31        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A5OD TCGA-B5-A5OE 
       11.70        11.87        12.79        62.14        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       18.61        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       48.56        23.47        43.30        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A187 TCGA-BG-A18A 
       28.54        56.58        14.83        12.56        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3PP 
       15.45        14.27        35.67        23.70        20.12         6.81 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
       34.98         6.21        10.22        24.99        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0UA 
        4.80        77.95        67.99        96.49        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       85.84        82.39        81.57        73.25        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZS TCGA-D1-A0ZU 
       49.55        66.48        19.79        29.95         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 
       29.88         1.91        29.33        32.58        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A179 TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       19.53         6.64         6.77         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
       28.01        28.08         1.51         1.78        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 
       22.92         1.41        13.22         0.72        18.25         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DG 
       15.06         1.05         3.95         3.52        44.88         4.27 
TCGA-D1-A3DH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT 
        4.11        39.29        36.62        24.30        35.38        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10        91.96        23.38        48.36        17.06         2.37 
TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.01        16.80        10.92         7.99        10.78        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH 
       35.05        33.01        27.12        32.28        32.38        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.36        35.15        12.89        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       16.34        14.99        24.36        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GW 
       13.97         6.90        18.84        17.62        15.81         8.55 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OQ TCGA-EY-A3L3 
       19.33        12.59        18.87        22.82        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       13.84        17.92         2.14        40.01        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        13.84         8.98        96.69         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-QS-A5YQ 
       25.02        26.01         1.74        13.15        10.82         4.21 
TCGA-QS-A5YR 
        5.52 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           117.99            191.84 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            20.28             23.70 
[1] "0.0 - 118.0 (20.3)" "0.1 - 191.8 (23.7)"
[1] "hr=" "1.5"
D2V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1Q GAIN MUTATED                                       128
  1Q GAIN WILD-TYPE                                     239
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1Q GAIN MUTATED                               5
  1Q GAIN WILD-TYPE                            15
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1Q GAIN MUTATED                                  32
  1Q GAIN WILD-TYPE                                66
D2V3, multiclass
                                         clus
vv                                        1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA             128               239
  MIXED SEROUS AND ENDOMETRIOID                         5                15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    32                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    46 119
  1Q GAIN WILD-TYPE  92 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     46  119
  1Q GAIN WILD-TYPE   92  228
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               46                92
  YES             119               228
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED   113   7   6  10
  1Q GAIN WILD-TYPE 223  15  11  19
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             113               223
  R1               7                15
  R2               6                11
  RX              10                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1     4
  1Q GAIN WILD-TYPE                                3    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q GAIN MUTATED                          26
  1Q GAIN WILD-TYPE                        47
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q GAIN MUTATED                                           2   128
  1Q GAIN WILD-TYPE                                         7   227
D2V6, multiclass
                                           clus
vv                                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                              26                47
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                 128               227
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     2 119
  1Q GAIN WILD-TYPE  11 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2  119
  1Q GAIN WILD-TYPE   11  217
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO             119               217
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    63  18
  2P GAIN WILD-TYPE 360  42
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               81               402 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               18                42 
$`2P GAIN MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0R7 TCGA-A5-A1OG 
      149.56        60.53        28.27        20.81        17.59        11.44 
TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BK 
       36.33        28.64        14.96         1.18         1.08         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05A 
        1.64         0.92         0.76        16.87         1.71        39.42 
TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05W 
       48.79        97.71        41.95        18.25        33.73        68.35 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H7 
       28.54        37.78        16.96        67.50         4.77        33.53 
TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3G3 TCGA-B5-A0JT TCGA-B5-A0K7 TCGA-B5-A0K9 
       17.75         2.96         0.03        43.13        17.10        11.01 
TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A0M0 TCGA-BG-A0M2 
       75.72        50.89        12.79         5.03        19.33        20.94 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A2AE TCGA-BG-A3PP 
        7.92        36.49        15.42        24.39        23.70         6.81 
TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI 
       35.90        10.16        24.13        16.64         4.80        61.87 
TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A168 
       72.72        63.58        49.55        19.79        29.95        36.10 
TCGA-D1-A16I TCGA-D1-A17R TCGA-D1-A1NW TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-DI-A1NN 
       11.51        11.15         0.72         8.48         4.11        35.38 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 
       91.96        48.36        32.38        26.96        22.26         6.21 
TCGA-EY-A1GH TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A214 TCGA-EY-A54A 
       23.34         6.90        19.27        15.09        14.40         3.72 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-K6-A3WQ 
       36.00         7.99        13.15 

$`2P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        38.37        36.82        23.21        68.65        19.96 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        91.04        46.32         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        7.33         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3EK 
        3.02         0.49         1.12         0.76         2.24        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26         1.28        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AP-A051 
       15.62         1.94        15.95         1.87         2.33        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D 
       21.99         5.95        23.31        86.07         8.22        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
       45.53        36.89         7.86        12.20        20.91       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       31.30        35.54        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        16.24         0.56        13.58        19.82        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.01        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 
       72.56        54.12        25.12        36.39        11.08        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       71.24        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        27.32        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.33         0.13         0.20        20.52         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18         8.35        14.47         0.13        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       46.75        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       191.84       102.31        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD 
       11.70        11.87        15.29        62.14        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       34.95        18.61        20.19        35.21        34.98        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV 
       43.04        39.32        30.81        21.17        20.28        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        35.67        20.12        11.31 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98         6.21        10.22        31.76        24.99        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 
       88.34        85.84        82.39        81.57        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       62.79        63.16        66.48        16.83         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         1.41         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02         6.77         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51         1.78        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       44.88         0.26         4.27        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       24.30         9.37        12.39        31.10        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       32.28        24.79        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       12.89        27.16        16.34        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.90        22.78        13.97 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.88        17.62        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 
        8.55         6.48        19.33        12.59         3.62        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        13.45        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       13.84         6.44        17.92         2.14         6.97         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       40.01        34.98        33.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        26.01 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       41.06         1.74         2.43        10.82         4.21         5.52 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.03              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           149.56            191.84 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           19.330            23.325 
[1] "0.0 - 149.6 (19.3)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.3"
D3V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2P GAIN MUTATED                                        40
  2P GAIN WILD-TYPE                                     327
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2P GAIN MUTATED                               5
  2P GAIN WILD-TYPE                            15
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2P GAIN MUTATED                                  38
  2P GAIN WILD-TYPE                                60
D3V3, multiclass
                                         clus
vv                                        2P GAIN MUTATED 2P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              40               327
  MIXED SEROUS AND ENDOMETRIOID                         5                15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    38                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    20  63
  2P GAIN WILD-TYPE 118 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     20   63
  2P GAIN WILD-TYPE  118  284
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               20               118
  YES              63               284
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED    58   3   5   5
  2P GAIN WILD-TYPE 278  19  12  24
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              58               278
  R1               3                19
  R2               5                12
  RX               5                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     5
  2P GAIN WILD-TYPE                                4    14
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P GAIN MUTATED                          13
  2P GAIN WILD-TYPE                        60
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P GAIN MUTATED                                           2    61
  2P GAIN WILD-TYPE                                         7   294
D3V6, multiclass
                                           clus
vv                                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   5                14
  BLACK OR AFRICAN AMERICAN                              13                60
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  61               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"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0  59
  2P GAIN WILD-TYPE  13 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   59
  2P GAIN WILD-TYPE   13  277
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                13
  NOT HISPANIC OR LATINO              59               277
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    52  14
  2Q GAIN WILD-TYPE 371  46
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               66               417 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               14                46 
$`2Q GAIN MUTATED`
TCGA-A5-A0GN TCGA-A5-A0GV TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K4 
       60.53        20.81        17.59        11.44        36.33        28.64 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3IA 
       14.96         1.18         1.08         1.68         1.64         0.92 
TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX 
        0.76         1.71        97.71        41.95        18.25        33.73 
TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3G3 TCGA-B5-A0JT 
       68.35        37.78        17.75         2.96         0.03        43.13 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A3S1 TCGA-BG-A0M2 
       17.10        11.01        75.72        50.89         5.03        20.94 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A2AE TCGA-BG-A3PP 
        7.92        36.49        15.42        24.39        23.70         6.81 
TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0UT 
       35.90        10.16        24.13        16.64         4.80        72.72 
TCGA-BS-A0V7 TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A168 TCGA-D1-A16I TCGA-D1-A17R 
       63.58        19.79        29.95        36.10        11.51        11.15 
TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A2CG 
        8.48         4.11        35.38        91.96        48.36        32.38 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GM TCGA-EY-A1GO 
       26.96        22.26         6.21        23.34         6.90        19.27 
TCGA-EY-A1GS TCGA-EY-A214 TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-K6-A3WQ 
       15.09        14.40         3.72        36.00         7.99        13.15 

$`2Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW 
       60.53        46.55        38.37        36.82        28.27        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        19.96        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       15.95         7.92         9.60         8.02        91.04        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.33         5.16         7.33         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.85         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        2.24        14.66        22.49        22.26         1.28        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       16.87         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y 
       16.24         0.56        13.58        19.82        29.69        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ 
       68.71        33.40        40.50        19.36        26.33        27.32 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
       14.47         0.13        80.38        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A0KB 
       25.91        23.01        17.88        13.74        17.85         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      191.84       102.31        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       15.29        12.79        62.14        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       18.61        20.19        19.33        35.21        34.98        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV 
       43.04        39.32        30.81        21.17        20.28        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        35.67        20.12        11.31 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98         6.21        10.22        31.76        24.99        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       67.20        88.34        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52        41.42        44.88         0.26         4.27 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT 
       16.31        39.29        36.62        24.30         9.37        12.39 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92         7.99        10.78        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       35.05        33.01        27.12        32.28        24.79        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KW 
       34.39        19.36        35.15        12.89        27.16        16.34 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       23.90        22.78        13.97        18.84        17.88        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       12.59         3.62        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       31.04        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        2.14         6.97         5.29        40.01        34.98        33.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 
       28.96        25.02        26.01        41.06         1.74         2.43 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.03              0.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            97.71            191.84 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            18.00             23.38 
[1] "0.0 - 97.7 (18.0)"  "0.1 - 191.8 (23.4)"
[1] "hr=" "2.3"
D4V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2Q GAIN MUTATED                                        34
  2Q GAIN WILD-TYPE                                     333
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2Q GAIN MUTATED                               4
  2Q GAIN WILD-TYPE                            16
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2Q GAIN MUTATED                                  29
  2Q GAIN WILD-TYPE                                69
D4V3, multiclass
                                         clus
vv                                        2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              34               333
  MIXED SEROUS AND ENDOMETRIOID                         4                16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    29                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    15  52
  2Q GAIN WILD-TYPE 123 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     15   52
  2Q GAIN WILD-TYPE  123  295
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               15               123
  YES              52               295
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED    45   2   5   5
  2Q GAIN WILD-TYPE 291  20  12  24
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              45               291
  R1               2                20
  R2               5                12
  RX               5                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     4
  2Q GAIN WILD-TYPE                                4    15
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q GAIN MUTATED                           8
  2Q GAIN WILD-TYPE                        65
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q GAIN MUTATED                                           1    52
  2Q GAIN WILD-TYPE                                         8   303
D4V6, multiclass
                                           clus
vv                                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   4                15
  BLACK OR AFRICAN AMERICAN                               8                65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  52               303
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  47
  2Q GAIN WILD-TYPE  13 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   47
  2Q GAIN WILD-TYPE   13  289
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                13
  NOT HISPANIC OR LATINO              47               289
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    28   9
  3P GAIN WILD-TYPE 395  51
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               37               446 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                9                51 
$`3P GAIN MUTATED`
TCGA-A5-A2K2 TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3IA TCGA-AJ-A3QS TCGA-AP-A0LO 
       91.04         0.49         2.24         0.92        16.87        33.40 
TCGA-AP-A1DO TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A1CA TCGA-AX-A2H4 TCGA-AX-A2H7 
       31.30        68.35        12.26        20.28        30.12        33.53 
TCGA-B5-A0K4 TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-BG-A0M4 TCGA-BG-A0RY 
       17.88        33.50       191.84        11.87        34.98        15.42 
TCGA-BG-A0W1 TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-D1-A2G5 TCGA-D1-A2G6 
       52.83        67.20        73.25        49.55        41.42         8.48 
TCGA-D1-A3DH TCGA-DI-A2QY TCGA-EO-A22Y TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GQ 
        4.11        91.96        24.79        26.96         4.54        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A4KR TCGA-FI-A2EW 
       17.62        15.09         8.55         3.62         6.44        59.01 
TCGA-FI-A2EX 
        9.07 

$`3P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33         9.60         8.02        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.16         7.33        14.96         1.18         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        0.39        19.79         0.85         2.40         3.02         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        0.76         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        1.28        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 
        1.94        15.95         1.87         1.71         2.33        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z 
        0.56        13.58        19.82        29.69        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        53.92        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.55        15.25        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       71.24        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.10         0.33         0.13         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.03         0.13         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.13        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       25.91        23.01        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       15.29        12.79        62.14         5.03        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       28.54        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       35.67        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        72.72        59.51        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02         6.77         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DA 
       15.06         1.05         3.95         3.52        44.88         0.26 
TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
        4.27        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
        9.37        12.39        31.10        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       32.28        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        22.26        16.34         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT 
       22.78        13.97         6.90        19.27        18.84        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       12.43        15.81         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        13.45        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       27.35        13.84        17.92         2.14         6.97         3.72 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.29        40.01        34.98        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       13.84         8.98        96.69        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC 
       26.01        41.06         1.74        13.15         2.43        10.82 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.49              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           191.84            185.79 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            20.28             22.87 
[1] "0.5 - 191.8 (20.3)" "0.0 - 185.8 (22.9)"
[1] "hr=" "2"  
D5V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3P GAIN MUTATED                                        23
  3P GAIN WILD-TYPE                                     344
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3P GAIN MUTATED                               0
  3P GAIN WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3P GAIN MUTATED                                  15
  3P GAIN WILD-TYPE                                83
D5V3, multiclass
                                         clus
vv                                        3P GAIN MUTATED 3P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              23               344
  MIXED SEROUS AND ENDOMETRIOID                         0                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    15                83
[1] 3 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, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     6  32
  3P GAIN WILD-TYPE 132 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6   32
  3P GAIN WILD-TYPE  132  315
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                6               132
  YES              32               315
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    24   4   2   3
  3P GAIN WILD-TYPE 312  18  15  26
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              24               312
  R1               4                18
  R2               2                15
  RX               3                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     0
  3P GAIN WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P GAIN MUTATED                           8
  3P GAIN WILD-TYPE                        65
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P GAIN MUTATED                                           3    24
  3P GAIN WILD-TYPE                                         6   331
D5V6, multiclass
                                           clus
vv                                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                               8                65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                  24               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"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     1  29
  3P GAIN WILD-TYPE  12 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   29
  3P GAIN WILD-TYPE   12  307
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              29               307
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    50  16
  3Q GAIN WILD-TYPE 373  44
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               66               417 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16                44 
$`3Q GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A3BD 
       37.02        11.44        36.33        91.04        14.96         0.49 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3QS TCGA-AP-A0L8 TCGA-AP-A0LO 
        2.24         1.64         0.92        16.87        48.79        33.40 
TCGA-AP-A1DO TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CR 
       31.30        68.35        12.26        20.28        76.83        11.08 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A3FW TCGA-B5-A0K4 TCGA-B5-A11I TCGA-B5-A11R 
       30.12        33.53         0.33        17.88        75.72        33.50 
TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0RY 
      191.84        11.87        12.79        34.98         7.92        15.42 
TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BK-A0CC TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UV 
       52.83        12.56        10.22         4.80        67.20        73.25 
TCGA-BS-A0V8 TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A1NW TCGA-D1-A2G5 TCGA-D1-A2G6 
       49.55        36.10        27.42         0.72        41.42         8.48 
TCGA-D1-A3DH TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A22Y 
        4.11        91.96        48.36         7.36        10.92        24.79 
TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GQ 
       32.38        26.96        16.34         4.54         6.90        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A3QX 
       17.62        15.09         8.55         3.62        13.45        13.84 
TCGA-EY-A4KR TCGA-FI-A2CX TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-K6-A3WQ 
        6.44        40.01        59.01         9.07        28.93        13.15 

$`3Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M 
       46.32        28.64         5.33         5.16         7.33         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.08         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        3.02         1.12         0.76         1.68        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26         1.28        36.99        20.65         1.35        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW 
        0.76         1.94        15.95         1.87         1.71         2.33 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       39.42        57.80        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z 
        0.56        13.58        19.82        29.69        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        53.92        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       13.55        15.25        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H8 
       67.50        25.12        36.39         4.77        71.24        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.13         0.20        20.52         0.03         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18         8.35        14.47         0.13        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        23.01        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       36.82        32.09        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       18.41        17.36        16.57       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       14.70        11.70        15.29        62.14         5.03        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       28.54        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
        6.21        10.16        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        37.32        36.36        37.51        36.79 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        1.41        13.22        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DA 
       15.06         1.05         3.95         3.52        44.88         0.26 
TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
        4.27        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
        9.37        12.39        31.10        23.38        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        6.67        16.01        16.80         7.99        10.78        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS 
       35.05        33.01        27.12        32.28        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1G7 
       19.36        35.15        12.89        27.16        22.26         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT 
       23.90        22.78        13.97        19.27        18.84        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       12.43        15.81         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       18.87        22.82        45.76        31.04        29.10        27.35 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       17.92         2.14         6.97         3.72         5.29        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 
       28.96        25.02        26.01        41.06         1.74         2.43 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.33              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           191.84            185.79 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           17.245            23.310 
[1] "0.3 - 191.8 (17.2)" "0.0 - 185.8 (23.3)"
[1] "hr=" "2.4"
D6V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3Q GAIN MUTATED                                        30
  3Q GAIN WILD-TYPE                                     337
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3Q GAIN MUTATED                               4
  3Q GAIN WILD-TYPE                            16
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3Q GAIN MUTATED                                  33
  3Q GAIN WILD-TYPE                                65
D6V3, multiclass
                                         clus
vv                                        3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              30               337
  MIXED SEROUS AND ENDOMETRIOID                         4                16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    33                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    17  50
  3Q GAIN WILD-TYPE 121 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     17   50
  3Q GAIN WILD-TYPE  121  297
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               17               121
  YES              50               297
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    43   5   5   5
  3Q GAIN WILD-TYPE 293  17  12  24
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              43               293
  R1               5                17
  R2               5                12
  RX               5                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  0     3
  3Q GAIN WILD-TYPE                                4    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q GAIN MUTATED                          16
  3Q GAIN WILD-TYPE                        57
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q GAIN MUTATED                                           3    40
  3Q GAIN WILD-TYPE                                         6   315
D6V6, multiclass
                                           clus
vv                                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                              16                57
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                  40               315
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     2  49
  3Q GAIN WILD-TYPE  11 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   49
  3Q GAIN WILD-TYPE   11  287
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO              49               287
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     9   3
  4P GAIN WILD-TYPE 414  57
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               471 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                57 
$`4P GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-AJ-A23N TCGA-AP-A0LI TCGA-B5-A0JN TCGA-BG-A0M6 
       37.02        11.44         1.08        97.71        80.38         7.92 
TCGA-BK-A139 TCGA-BK-A4ZD TCGA-D1-A3DH TCGA-EO-A1Y5 TCGA-EO-A2CG TCGA-EY-A1GW 
       10.16        16.64         4.11        10.92        32.38         8.55 

$`4P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ 
       29.06        42.35        15.95         7.92        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33        14.96         1.18         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.85         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        2.24         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
        1.28         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
        0.76         1.94        15.95         1.87        16.87         1.71 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.33        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        18.25        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        8.35        14.47         0.13        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       12.79        62.14         5.03        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        35.67        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98         6.21        10.22        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        67.20        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH 
       41.42         8.48        44.88         0.26         4.27        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10        91.96        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
        6.67        16.01         7.36        16.80         7.99        10.78 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        32.28        24.79 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        19.36        35.15        12.89        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       26.96        22.26        16.34         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        15.09        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       19.33        12.59         3.62        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       13.45        45.76        31.04        29.10        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
        6.44        17.92         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        34.98        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       25.02        26.01        41.06         1.74        13.15         2.43 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             1.08              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            97.71            191.84 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            11.18             23.01 
[1] "1.1 - 97.7 (11.2)"  "0.0 - 191.8 (23.0)"
[1] "hr=" "2.6"
D7V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4P GAIN MUTATED                                         4
  4P GAIN WILD-TYPE                                     363
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4P GAIN MUTATED                               0
  4P GAIN WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4P GAIN MUTATED                                   8
  4P GAIN WILD-TYPE                                90
D7V3, multiclass
                                         clus
vv                                        4P GAIN MUTATED 4P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               4               363
  MIXED SEROUS AND ENDOMETRIOID                         0                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     8                90
[1] 3 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, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4   8
  4P GAIN WILD-TYPE 134 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    8
  4P GAIN WILD-TYPE  134  339
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                4               134
  YES               8               339
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     8   1   2   0
  4P GAIN WILD-TYPE 328  21  15  29
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               8               328
  R1               1                21
  R2               2                15
  RX               0                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     2
  4P GAIN WILD-TYPE                                4    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P GAIN MUTATED                           4
  4P GAIN WILD-TYPE                        69
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P GAIN MUTATED                                           0     5
  4P GAIN WILD-TYPE                                         9   350
D7V6, multiclass
                                           clus
vv                                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               4                69
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                   5               350
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1   6
  4P GAIN WILD-TYPE  12 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    6
  4P GAIN WILD-TYPE   12  330
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO               6               330
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     7   1
  4Q GAIN WILD-TYPE 416  59
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8               475 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                59 
$`4Q GAIN MUTATED`
TCGA-A5-A0G5 TCGA-AX-A3G3 TCGA-B5-A0K8 TCGA-BK-A139 TCGA-BK-A4ZD TCGA-EO-A1Y5 
       37.02         0.03        17.85        10.16        16.64        10.92 
TCGA-EO-A2CG TCGA-EY-A1GW 
       32.38         8.55 

$`4Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.16         7.33        14.96         1.18         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79         0.85         2.40         3.02         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76         2.24         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26         1.28         0.92        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
        1.35        15.62         0.76         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       16.87         1.71         2.33        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89         7.86        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       36.39        11.08         4.77        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.10         0.33         0.13         0.20        20.52         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         1.18         8.35        14.47         0.13        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       11.87        15.29        12.79        62.14         5.03        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       10.22        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80         7.99        10.78        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       33.01        27.12        32.28        24.79        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.36        35.15        12.89        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
        6.90        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        15.81         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
        3.62        14.40        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       31.04        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         3.72         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        26.01 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ 
       41.06         1.74        13.15         2.43        10.82         4.21 
TCGA-QS-A5YR 
        5.52 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.03              0.10 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            37.02            191.84 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            13.78             23.01 
[1] "0.0 - 37.0 (13.8)"  "0.1 - 191.8 (23.0)"
[1] "hr=" "1.5"
D8V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4Q GAIN MUTATED                                         3
  4Q GAIN WILD-TYPE                                     364
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4Q GAIN MUTATED                               0
  4Q GAIN WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4Q GAIN MUTATED                                   5
  4Q GAIN WILD-TYPE                                93
D8V3, multiclass
                                         clus
vv                                        4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               3               364
  MIXED SEROUS AND ENDOMETRIOID                         0                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     5                93
[1] 3 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, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   7
  4Q GAIN WILD-TYPE 137 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    7
  4Q GAIN WILD-TYPE  137  340
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1               137
  YES               7               340
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     5   1   0   0
  4Q GAIN WILD-TYPE 331  21  17  29
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               5               331
  R1               1                21
  R2               0                17
  RX               0                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     1
  4Q GAIN WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q GAIN MUTATED                           2
  4Q GAIN WILD-TYPE                        71
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q GAIN MUTATED                                           0     4
  4Q GAIN WILD-TYPE                                         9   351
D8V6, multiclass
                                           clus
vv                                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               2                71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                   4               351
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1   3
  4Q GAIN WILD-TYPE  12 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    3
  4Q GAIN WILD-TYPE   12  333
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO               3               333
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    35  12
  5P GAIN WILD-TYPE 388  48
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               47               436 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12                48 
$`5P GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OH TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3IA 
       37.02        36.33        14.96         1.08         0.39         0.92 
TCGA-AJ-A3NH TCGA-AP-A05H TCGA-AP-A0LH TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AX-A0IS 
        0.76        45.53        36.36        31.30        41.95        35.01 
TCGA-AX-A0IW TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3G3 TCGA-AX-A3GI 
       37.78         4.77        71.24         2.96         0.03         0.13 
TCGA-B5-A1MY TCGA-B5-A5OD TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0VT TCGA-BG-A18C 
       11.87        34.13        35.21         7.92        24.39        15.45 
TCGA-BK-A139 TCGA-BS-A0TE TCGA-BS-A0TI TCGA-D1-A16N TCGA-D1-A1NW TCGA-D1-A3DH 
       10.16         4.80        61.87        31.07         0.72         4.11 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       35.38         9.37        12.39        48.36        10.92        10.78 
TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A547 
       26.96         4.54        17.62        15.09        13.45        17.92 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       36.00        59.01         9.07        28.93        25.02 

$`5P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95         7.92        11.44         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        7.33         1.18         1.97        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        3.02         0.49         1.12         0.76         2.24         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.64        14.66        22.49        22.26         1.28        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       16.87         1.71         2.33        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J 
       23.31        86.07         8.22        39.42        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        60.36        55.89        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       18.25        33.73         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        28.54        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       36.39        11.08        30.12        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC 
       14.40        14.70        11.70        15.29        12.79        62.14 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
        5.03        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        34.98        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        21.17        20.28        15.42        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        35.67        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98         6.21        10.22        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       23.47        85.55        78.21        77.95        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        67.20        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       11.51        29.92        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02         6.77         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       13.22        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        0.26         4.27        16.31        39.29        36.62        24.30 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        91.96        23.38        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
       16.01         7.36        16.80         7.99        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       33.01        27.12        32.28        24.79        32.38        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU 
       34.39        19.36        35.15        12.89        27.16        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       16.34         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        17.88        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
        8.55         6.48        19.33        12.59         3.62        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       18.87        22.82        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       13.84         6.44         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        34.98        33.99         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ 
       96.69        28.96        26.01        41.06         1.74        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        2.43        10.82         4.21         5.52 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            71.24            191.84 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            15.45             23.11 
[1] "0.0 - 71.2 (15.4)"  "0.1 - 191.8 (23.1)"
[1] "hr=" "2.9"
D9V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5P GAIN MUTATED                                        16
  5P GAIN WILD-TYPE                                     351
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5P GAIN MUTATED                               3
  5P GAIN WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5P GAIN MUTATED                                  28
  5P GAIN WILD-TYPE                                70
D9V3, multiclass
                                         clus
vv                                        5P GAIN MUTATED 5P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              16               351
  MIXED SEROUS AND ENDOMETRIOID                         3                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    28                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     8  39
  5P GAIN WILD-TYPE 130 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      8   39
  5P GAIN WILD-TYPE  130  308
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                8               130
  YES              39               308
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED    34   2   5   2
  5P GAIN WILD-TYPE 302  20  12  27
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              34               302
  R1               2                20
  R2               5                12
  RX               2                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  1     1
  5P GAIN WILD-TYPE                                3    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P GAIN MUTATED                          13
  5P GAIN WILD-TYPE                        60
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P GAIN MUTATED                                           0    29
  5P GAIN WILD-TYPE                                         9   326
D9V6, multiclass
                                           clus
vv                                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                              13                60
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  29               326
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     2  32
  5P GAIN WILD-TYPE  11 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   32
  5P GAIN WILD-TYPE   11  304
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO              32               304
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    14   4
  5Q GAIN WILD-TYPE 409  56
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               18               465 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                56 
$`5Q GAIN MUTATED`
TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AX-A0IS TCGA-AX-A3G3 TCGA-B5-A1MY TCGA-BG-A0VT 
       31.30        41.95        35.01         0.03        11.87        24.39 
TCGA-BG-A18C TCGA-BS-A0TE TCGA-D1-A16N TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 
       15.45         4.80        31.07        35.38        48.36        10.92 
TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GS TCGA-FI-A2EW TCGA-FI-A2EY 
       26.96         4.54        17.62        15.09        59.01        28.93 

$`5Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        0.49         1.12         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26         1.28         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65         1.35        15.62         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
        1.87        16.87         1.71         2.33        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89         7.86        12.20        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       60.36        55.89        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IW 
       51.09        27.39        30.02        60.66        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.13         0.20        20.52         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       12.79        62.14         5.03        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       35.67        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       23.47        85.55        78.21        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        67.20        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        11.51        29.92        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH 
        8.48        44.88         0.26         4.27         4.11        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       91.96        23.38        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80         7.99        10.78        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       33.01        27.12        32.28        24.79        32.38        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU 
       34.39        19.36        35.15        12.89        27.16        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       16.34         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        17.88        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
        8.55         6.48        19.33        12.59         3.62        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        13.45        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84         6.44        17.92         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
        3.72         5.29        40.01        34.98        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2F4 
        7.99        13.84         8.98        96.69         9.07        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       25.02        26.01        41.06         1.74        13.15         2.43 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            59.01            191.84 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           25.675            22.780 
[1] "0.0 - 59.0 (25.7)"  "0.1 - 191.8 (22.8)"
[1] "hr=" "2"  
D10V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5Q GAIN MUTATED                                         8
  5Q GAIN WILD-TYPE                                     359
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5Q GAIN MUTATED                               0
  5Q GAIN WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5Q GAIN MUTATED                                  10
  5Q GAIN WILD-TYPE                                88
D10V3, multiclass
                                         clus
vv                                        5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               8               359
  MIXED SEROUS AND ENDOMETRIOID                         0                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    10                88
[1] 3 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, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     3  15
  5Q GAIN WILD-TYPE 135 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3   15
  5Q GAIN WILD-TYPE  135  332
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                3               135
  YES              15               332
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    12   1   2   1
  5Q GAIN WILD-TYPE 324  21  15  28
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              12               324
  R1               1                21
  R2               2                15
  RX               1                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q GAIN MUTATED                           5
  5Q GAIN WILD-TYPE                        68
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q GAIN MUTATED                                           0    10
  5Q GAIN WILD-TYPE                                         9   345
D10V6, multiclass
                                           clus
vv                                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               5                68
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  10               345
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  12
  5Q GAIN WILD-TYPE  13 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   12
  5Q GAIN WILD-TYPE   13  324
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                13
  NOT HISPANIC OR LATINO              12               324
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    60   9
  6P GAIN WILD-TYPE 363  51
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               69               414 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                9                51 
$`6P GAIN MUTATED`
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       11.44        36.33         1.18         0.49         1.12         2.24 
TCGA-AJ-A3IA TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A5FX 
        0.92        48.79        97.71        33.40        41.95        33.73 
TCGA-AX-A06J TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H7 
       30.02        37.78        20.28        12.43        76.83        33.53 
TCGA-AX-A2HA TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN 
       68.71         0.13        20.52         0.03         0.13        80.38 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MU 
        4.11         8.71        75.72        33.50        27.35        50.89 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A0C9 
       12.79         5.03        34.13        36.49        15.45        35.90 
TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A168 
       10.22        24.13        16.64        67.20        49.55        36.10 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO 
       31.07        18.67        41.42         4.11        35.38         9.37 
TCGA-DI-A2QY TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       91.96        24.79        32.38        26.96        22.26        16.34 
TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A214 TCGA-EY-A2ON 
        4.54        19.27        17.88        17.62        14.40        13.45 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2EW 
       27.35        13.84         3.72        40.01        33.99        59.01 
TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-K6-A3WQ 
       28.93        26.01        13.15 

$`6P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ 
       24.62        29.06        42.35        15.95         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33        14.96         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        0.85         2.40         3.02         0.76         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26         1.28        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
        1.35        15.62         0.76         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       16.87         1.71         2.33        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        12.20        20.91       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       27.12        82.52        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       18.25         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       53.92        12.26        51.09        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       16.96        13.55        15.25        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       71.24        61.18        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.10         0.33         0.20         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        8.35        14.47        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       11.01       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V 
       43.96        40.50        36.82        32.09        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FC 
       14.40        14.70        11.70        11.87        15.29        62.14 
TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98         7.92        38.37        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       12.56        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
        6.81        34.98         6.21        10.16        31.76        24.99 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O 
       37.51        36.79        27.42        11.51        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU 
        8.48        44.88         0.26         4.27        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       36.62        24.30        12.39        31.10        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       27.12        32.28        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       12.89        27.16         6.21        14.99         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
        6.90        18.84        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 
        8.55         6.48        19.33        12.59         3.62        18.87 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 
       22.82        45.76        31.04        29.10         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2D4 
        2.14         6.97         5.29        34.98        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 
       13.84         8.98        96.69         9.07        28.96        25.02 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       41.06         1.74         2.43        10.82         4.21         5.52 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.03              0.10 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            97.71            191.84 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           24.790            22.665 
[1] "0.0 - 97.7 (24.8)"  "0.1 - 191.8 (22.7)"
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6P GAIN MUTATED                                        34
  6P GAIN WILD-TYPE                                     333
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6P GAIN MUTATED                               1
  6P GAIN WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6P GAIN MUTATED                                  34
  6P GAIN WILD-TYPE                                64
D11V3, multiclass
                                         clus
vv                                        6P GAIN MUTATED 6P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              34               333
  MIXED SEROUS AND ENDOMETRIOID                         1                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    34                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    17  52
  6P GAIN WILD-TYPE 121 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     17   52
  6P GAIN WILD-TYPE  121  295
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               17               121
  YES              52               295
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    41   2   3   7
  6P GAIN WILD-TYPE 295  20  14  22
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              41               295
  R1               2                20
  R2               3                14
  RX               7                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     2
  6P GAIN WILD-TYPE                                4    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P GAIN MUTATED                          19
  6P GAIN WILD-TYPE                        54
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P GAIN MUTATED                                           2    42
  6P GAIN WILD-TYPE                                         7   313
D11V6, multiclass
                                           clus
vv                                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                              19                54
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  42               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"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     1  44
  6P GAIN WILD-TYPE  12 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1   44
  6P GAIN WILD-TYPE   12  292
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              44               292
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    49   7
  6Q GAIN WILD-TYPE 374  53
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               56               427 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                7                53 
$`6Q GAIN MUTATED`
TCGA-AJ-A23M TCGA-AJ-A3BI TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ 
        1.18         2.24        48.79        97.71        33.40        41.95 
TCGA-AP-A5FX TCGA-AX-A06J TCGA-AX-A0IW TCGA-AX-A1CC TCGA-AX-A2H7 TCGA-AX-A2HA 
       33.73        30.02        37.78        12.43        33.53        68.71 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0KB 
        0.33         0.13        20.52         0.13        80.38         4.11 
TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3S1 
        8.71        75.72        33.50        50.89        12.79         5.03 
TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A26L 
       34.13        36.49        15.45        35.90        10.22        24.13 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A168 TCGA-D1-A16N TCGA-D1-A16S 
       16.64        67.20        49.55        36.10        31.07        18.67 
TCGA-D1-A2G5 TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A22Y TCGA-EO-A2CG 
       41.42        35.38        91.96        48.36        24.79        32.38 
TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       22.26         4.54        19.27        17.88        17.62        15.09 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2D0 
       14.40        13.45        27.35         3.72        40.01        33.99 
TCGA-FI-A2EW TCGA-FI-A2F8 
       59.01        25.02 

$`6Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O 
        5.33         5.16         7.33        14.96         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79         0.85         2.40         3.02         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        12.20        20.91       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       12.26        51.09        27.39        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.55        15.25        20.28        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       30.12        71.24        61.18        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.23         0.10         0.20         0.03         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18         8.35        14.47        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       17.85        11.01       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S 
       45.90        43.96        40.50        36.82        32.09        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      191.84       102.31        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       15.29        62.14        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31         6.81        34.98         6.21        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.76        24.99        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       29.92        33.63        10.65         0.69         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
        4.11        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       12.39        31.10        23.38        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.01         7.36        16.80        10.92         7.99        10.78 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH 
       31.96        35.05        33.01        27.12        32.28        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
       34.39        19.36        35.15        12.89        27.16        26.96 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       16.34         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       18.84        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
       19.33        12.59         3.62        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       31.04        29.10        13.84         6.44        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
        6.97         5.29        34.98        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F9 
        8.98        96.69         9.07        28.93        28.96        26.01 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ 
       41.06         1.74        13.15         2.43        10.82         4.21 
TCGA-QS-A5YR 
        5.52 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.13              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            97.71            191.84 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           28.685            22.260 
[1] "0.1 - 97.7 (28.7)"  "0.0 - 191.8 (22.3)"
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6Q GAIN MUTATED                                        30
  6Q GAIN WILD-TYPE                                     337
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6Q GAIN MUTATED                               1
  6Q GAIN WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6Q GAIN MUTATED                                  25
  6Q GAIN WILD-TYPE                                73
D12V3, multiclass
                                         clus
vv                                        6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              30               337
  MIXED SEROUS AND ENDOMETRIOID                         1                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    25                73
[1] 3 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, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    17  39
  6Q GAIN WILD-TYPE 121 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     17   39
  6Q GAIN WILD-TYPE  121  308
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               17               121
  YES              39               308
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    32   1   3   6
  6Q GAIN WILD-TYPE 304  21  14  23
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              32               304
  R1               1                21
  R2               3                14
  RX               6                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     1
  6Q GAIN WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q GAIN MUTATED                          19
  6Q GAIN WILD-TYPE                        54
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q GAIN MUTATED                                           2    32
  6Q GAIN WILD-TYPE                                         7   323
D12V6, multiclass
                                           clus
vv                                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                              19                54
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  32               323
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     1  36
  6Q GAIN WILD-TYPE  12 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1   36
  6Q GAIN WILD-TYPE   12  300
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              36               300
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    46  11
  7P GAIN WILD-TYPE 377  49
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               57               426 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               11                49 
$`7P GAIN MUTATED`
TCGA-A5-A0GV TCGA-A5-A3LO TCGA-AJ-A2QN TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       20.81         7.33         2.40         1.12         2.24         1.64 
TCGA-AJ-A3IA TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0L9 TCGA-AP-A0LI 
        0.92        15.62         0.76        57.80       125.42        97.71 
TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AX-A05W TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
       33.40        18.25        68.35         0.20        20.52         0.03 
TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A1MV TCGA-B5-A1MY 
       56.91        43.13        28.34        17.88        14.40        11.87 
TCGA-BG-A0M3 TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A2AE 
       35.21        30.81        15.42        24.39        12.56        23.70 
TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI 
       35.90        10.16        24.13        16.64         4.80        61.87 
TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A17C TCGA-D1-A17R TCGA-D1-A1NY 
       72.72        49.55        22.55         0.99        11.15        16.87 
TCGA-D1-A2G6 TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GL 
        8.48        10.92        24.79         6.21        23.34        13.97 
TCGA-EY-A1GO TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A2ON TCGA-EY-A549 TCGA-EY-A54A 
       19.27         8.55         6.48        13.45         6.97         3.72 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-K6-A3WQ 
       36.00        96.69        13.15 

$`7P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16        14.96         1.18         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BK 
       19.79         0.85         3.02         0.49         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26         1.28        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
        1.35         1.94        15.95         1.87        16.87         1.71 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.33        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91        48.79       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       36.36        31.73        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO 
       30.90        10.42        27.85        16.24        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        19.82        29.69        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.13         0.13         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
        0.13        80.38        46.75        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 
       32.55        28.64        30.51        25.91        23.01        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 
      102.31        50.89        14.70        11.70        15.29        12.79 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       62.14         5.03        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       20.19        19.33        20.94        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV 
       43.30        43.04        39.32        21.17        20.28        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        1.81         9.57        35.67        20.12        11.31         6.81 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98         6.21        10.22        31.76        24.99        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 
       88.34        85.84        82.39        81.57        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D 
       30.15        18.02         6.77         1.58         7.00        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
        1.78        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        18.25        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52        41.42        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
        4.11        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10        91.96        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       32.28        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G8 
       12.89        27.16        26.96        22.26        16.34        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ 
        4.54         8.15        24.36        27.16        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       22.78         6.90        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       16.11        12.43        15.81        19.33        12.59         3.62 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       14.40        18.87        22.82        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A5W2 
       27.35        13.84         6.44        17.92         2.14         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        34.98        33.99         7.99        13.84         8.98 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        26.01 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       41.06         1.74         2.43        10.82         4.21         5.52 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.03              0.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           125.42            191.84 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            16.64             23.47 
[1] "0.0 - 125.4 (16.6)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2"  
D13V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7P GAIN MUTATED                                        38
  7P GAIN WILD-TYPE                                     329
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7P GAIN MUTATED                               4
  7P GAIN WILD-TYPE                            16
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7P GAIN MUTATED                                  16
  7P GAIN WILD-TYPE                                82
D13V3, multiclass
                                         clus
vv                                        7P GAIN MUTATED 7P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              38               329
  MIXED SEROUS AND ENDOMETRIOID                         4                16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    16                82
[1] 3 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, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    13  45
  7P GAIN WILD-TYPE 125 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     13   45
  7P GAIN WILD-TYPE  125  302
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               13               125
  YES              45               302
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED    39   2   3   2
  7P GAIN WILD-TYPE 297  20  14  27
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              39               297
  R1               2                20
  R2               3                14
  RX               2                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  0     2
  7P GAIN WILD-TYPE                                4    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P GAIN MUTATED                           6
  7P GAIN WILD-TYPE                        67
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P GAIN MUTATED                                           1    45
  7P GAIN WILD-TYPE                                         8   310
D13V6, multiclass
                                           clus
vv                                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               6                67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  45               310
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     1  43
  7P GAIN WILD-TYPE  12 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1   43
  7P GAIN WILD-TYPE   12  293
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              43               293
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    42  13
  7Q GAIN WILD-TYPE 381  47
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               55               428 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               13                47 
$`7Q GAIN MUTATED`
TCGA-A5-A0GV TCGA-A5-A3LP TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3IA 
       20.81        14.96         2.40         2.24         1.64         0.92 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO 
       15.62         0.76        48.79       125.42        97.71        33.40 
TCGA-AP-A3K1 TCGA-AX-A05W TCGA-AX-A2HJ TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
       18.25        68.35        27.32         0.20        20.52         0.03 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A1MU 
        0.13        56.91        43.13        28.34        17.88        50.89 
TCGA-B5-A1MV TCGA-B5-A1MY TCGA-BG-A0M3 TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0VT 
       14.40        11.87        35.21        30.81        15.42        24.39 
TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT 
       23.70        35.90        16.64         4.80        61.87        72.72 
TCGA-D1-A0ZN TCGA-D1-A0ZZ TCGA-D1-A17C TCGA-D1-A17R TCGA-D1-A1NY TCGA-D1-A2G6 
       16.83        22.55         0.99        11.15        16.87         8.48 
TCGA-EC-A1NJ TCGA-EO-A22Y TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GL TCGA-EY-A1GO 
       16.01        24.79         6.21        23.34        13.97        19.27 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A549 TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EY 
        8.55         6.48         6.97         3.72        36.00        28.93 
TCGA-K6-A3WQ 
       13.15 

$`7Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33         1.18         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         0.85         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.68        14.66        22.49        22.26         1.28        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       20.65         1.35         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
        7.86        12.20        20.91       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
        6.71        30.90        10.42        27.85        16.24        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z 
        0.56        13.58        19.82        29.69        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.13         0.13         0.23         1.18         8.35        14.47 
TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       80.38        46.75        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.64        30.51        25.91        23.01        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 
       14.70        11.70        15.29        12.79        62.14         5.03 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       20.94        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       39.32        21.17        20.28        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA 
        9.57        35.67        20.12        11.31         6.81        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       78.21        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       67.20        88.34        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.51         1.78        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       13.22         0.72        18.25        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95         3.52        41.42        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27         4.11        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       35.38         9.37        12.39        31.10        91.96        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EC-A24G 
       48.36        17.06         2.37         6.67         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       27.12        32.28        32.38        19.40        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        12.89        27.16        26.96        22.26        16.34 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       23.90        22.78         6.90        18.84        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A210 
       15.09        16.11        12.43        15.81        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
        3.62        14.40        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       31.04        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        2.14         5.29        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 
       13.84         8.98        96.69        59.01         9.07        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC 
       25.02        26.01        41.06         1.74         2.43        10.82 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.03              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           125.42            191.84 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           16.870            23.425 
[1] "0.0 - 125.4 (16.9)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.6"
D14V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7Q GAIN MUTATED                                        38
  7Q GAIN WILD-TYPE                                     329
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7Q GAIN MUTATED                               4
  7Q GAIN WILD-TYPE                            16
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7Q GAIN MUTATED                                  14
  7Q GAIN WILD-TYPE                                84
D14V3, multiclass
                                         clus
vv                                        7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              38               329
  MIXED SEROUS AND ENDOMETRIOID                         4                16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    14                84
[1] 3 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, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    11  45
  7Q GAIN WILD-TYPE 127 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     11   45
  7Q GAIN WILD-TYPE  127  302
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               11               127
  YES              45               302
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED    38   1   2   1
  7Q GAIN WILD-TYPE 298  21  15  28
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              38               298
  R1               1                21
  R2               2                15
  RX               1                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0     3
  7Q GAIN WILD-TYPE                                4    16
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q GAIN MUTATED                           7
  7Q GAIN WILD-TYPE                        66
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q GAIN MUTATED                                           0    44
  7Q GAIN WILD-TYPE                                         9   311
D14V6, multiclass
                                           clus
vv                                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   3                16
  BLACK OR AFRICAN AMERICAN                               7                66
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  44               311
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     1  41
  7Q GAIN WILD-TYPE  12 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   41
  7Q GAIN WILD-TYPE   12  295
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              41               295
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    88  18
  8P GAIN WILD-TYPE 335  42
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              106               377 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               18                42 
$`8P GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OJ 
       37.02       105.37        23.21        17.59        11.44         9.60 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BD 
        7.33        14.96         0.39        19.79         2.40         0.49 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NE TCGA-AJ-A3NG 
        1.68         1.64        22.26         0.92        20.65        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LO 
        0.76         1.87        16.87       125.42       117.99        33.40 
TCGA-AP-A1DO TCGA-AP-A1E0 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A1CA TCGA-AX-A1CI 
       31.30        30.90        18.25        33.73        20.28        72.56 
TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A3FT 
       67.50         4.77        33.53        68.71        33.40         0.10 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11Q 
        0.20        20.52        43.13        17.88         8.71        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MW TCGA-B5-A5OE 
       33.50        27.35        19.56       191.84        14.70        34.95 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MQ 
       19.33        20.94        34.98        28.27        10.72        39.32 
TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45         1.81        23.70        35.90         6.21        10.22 
TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U9 TCGA-BS-A0UV 
       16.64        46.95         4.80        77.95        67.20        73.25 
TCGA-BS-A0VI TCGA-D1-A0ZU TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A168 
       63.16        28.67         4.44        39.48         0.66        36.10 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A17R 
       37.32        11.51        31.07         0.69        18.67        11.15 
TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-DI-A1C3 TCGA-DI-A2QU 
        2.07         3.52        41.42         8.48        24.30        31.10 
TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A2CH 
       17.06        10.92        10.78        33.01        24.79        19.40 
TCGA-EO-A3AZ TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ 
       27.16        14.99         4.54         6.90        19.27        17.88 
TCGA-EY-A1GR TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ 
       17.62         6.48        19.33        22.82        13.45        29.10 
TCGA-EY-A549 TCGA-FI-A2D4 TCGA-FI-A2F9 TCGA-K6-A3WQ 
        6.97         7.99        26.01        13.15 

$`8P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78         3.22 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
       87.32        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX 
       46.55        38.37        36.82        28.27        20.81        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.96        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
        7.92        36.33         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QM 
        5.33         5.16         1.18         1.08         1.97         0.85 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3EK TCGA-AJ-A3EL 
        3.02         1.12         0.76         2.24        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3TW 
        1.28        36.99         1.35         1.94        15.95         1.71 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.33        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       12.20        20.91        48.79       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        35.54        41.95        49.15         6.71 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       10.42        27.85        16.24         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CN 
       15.25        12.43        20.05        76.83        54.12        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HD 
       36.39        11.08        30.12        71.24        61.18        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        27.32         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G3 TCGA-AX-A3G4 
       38.70         0.23         0.33         0.13         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         1.18         8.35        14.47         0.13        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        46.75        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        23.01        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         4.11       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       36.82        16.73        19.50        18.41        17.36        16.57 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
      102.31        50.89        14.40        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       12.79        62.14         5.03        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0MC 
       20.19        35.21         7.92        38.37        36.49        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        14.27         9.57        35.67 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A139 TCGA-BK-A13B 
       20.12        11.31         6.81        34.98        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA 
       24.99        24.13        13.18        10.03         9.86        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       85.55        78.21        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        49.55        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV 
       19.79        29.95         8.55         0.56         4.87        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A16B TCGA-D1-A16D 
        3.68        29.33        32.58        15.72        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16V 
       36.79        27.42        29.92        33.63        10.65         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27         4.11        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX 
       36.62        35.38         9.37        12.39        91.96        23.38 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       48.36         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
        7.99        31.96        35.05        27.12        32.28        32.38 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU 
       34.39        19.36        35.15        12.89        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       16.34         6.21         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GS 
       23.34        23.90        22.78        13.97        18.84        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 
       16.11        12.43        15.81         8.55        12.59         3.62 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       14.40        18.87        45.76        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
        6.44        17.92         2.14         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       34.98        33.99        36.00        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV 
       59.01         9.07        28.93        28.96        25.02        41.06 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74         2.43        10.82         4.21         5.52 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.10              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           191.84            185.79 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            19.33             23.93 
[1] "0.1 - 191.8 (19.3)" "0.0 - 185.8 (23.9)"
[1] "hr=" "1.8"
D15V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8P GAIN MUTATED                                        79
  8P GAIN WILD-TYPE                                     288
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8P GAIN MUTATED                               6
  8P GAIN WILD-TYPE                            14
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8P GAIN MUTATED                                  22
  8P GAIN WILD-TYPE                                76
D15V3, multiclass
                                         clus
vv                                        8P GAIN MUTATED 8P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              79               288
  MIXED SEROUS AND ENDOMETRIOID                         6                14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    22                76
[1] 3 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, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    23  84
  8P GAIN WILD-TYPE 115 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     23   84
  8P GAIN WILD-TYPE  115  263
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               23               115
  YES              84               263
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    76   1   5   7
  8P GAIN WILD-TYPE 260  21  12  22
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              76               260
  R1               1                21
  R2               5                12
  RX               7                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     6
  8P GAIN WILD-TYPE                                4    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P GAIN MUTATED                          16
  8P GAIN WILD-TYPE                        57
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P GAIN MUTATED                                           3    76
  8P GAIN WILD-TYPE                                         6   279
D15V6, multiclass
                                           clus
vv                                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   6                13
  BLACK OR AFRICAN AMERICAN                              16                57
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                  76               279
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2  80
  8P GAIN WILD-TYPE  11 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   80
  8P GAIN WILD-TYPE   11  256
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO              80               256
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   113  25
  8Q GAIN WILD-TYPE 310  35
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              138               345 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               25                35 
$`8Q GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A1OG 
       37.02       105.37        65.75        23.21        17.59        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK 
       36.33         9.60        28.64         7.33        14.96         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       19.79         2.40         0.49         2.24         1.68         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH 
       22.26         1.28         0.92        20.65        15.62         0.76 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
        1.87        16.87        39.42        45.53        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1E0 TCGA-AP-A3K1 
      117.99         3.39        33.40        31.30        30.90        18.25 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC 
       33.73         0.56        37.78        13.55        20.28        12.43 
TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA 
       72.56        67.50         4.77        30.12        33.53        68.71 
TCGA-AX-A2HC TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-B5-A0JT TCGA-B5-A0K4 
       33.40         0.10         0.20        20.52        43.13        17.88 
TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V 
        8.71        88.34        32.09        33.50        27.35        19.56 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MW TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M0 
      191.84       102.31        14.70        34.13        34.95        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        34.98         7.92        36.49        28.27        10.72 
TCGA-BG-A0MT TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A0CB 
       21.17        15.45         1.81        23.70        35.90         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TE TCGA-BS-A0TG 
       10.22        10.16        16.64        46.95         4.80        77.95 
TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0VI TCGA-D1-A0ZP TCGA-D1-A0ZU TCGA-D1-A0ZZ 
       67.20        73.25        63.16        29.95        28.67        22.55 
TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16I 
        4.44        39.48         0.66        36.10        37.32        11.51 
TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1O0 
       31.07         0.69        18.67        11.15        13.22         2.07 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1C3 
        3.52        41.42         8.48        44.88         4.11        24.30 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       31.10        91.96        48.36        17.06        10.92         7.99 
TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 
       10.78        33.01        24.79        19.40        27.16        26.96 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR 
       14.99         4.54         6.90        19.27        17.88        17.62 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ 
       15.81         6.48        19.33        22.82        13.45        29.10 
TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2D4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-K6-A3WQ 
       17.92         6.97         7.99        26.01        41.06        13.15 

$`8Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78         3.22 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       87.32        74.10        57.53        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        36.82        28.27        20.81        68.65        19.96 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M 
        8.02        91.04        46.32         5.33         5.16         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
        1.08         1.97         0.85         3.02         1.12         0.76 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       14.66        22.49        36.99         1.35         1.94        15.95 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07         8.22        57.80        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
       20.91       110.37        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       83.97        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        60.36        55.89        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       41.95        49.15         6.71        10.42        27.85        16.24 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A1CP 
       15.25        20.05        76.83        54.12        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       11.08        71.24        61.18        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.33         0.13         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        23.01        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J 
       11.01         4.11       185.79       113.36        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W 
       45.90        43.96        40.50        36.82        16.73        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MX 
       18.41        17.36        16.57        50.89        14.40        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       11.87        15.29        12.79        62.14         5.03        41.06 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MG 
       18.61        20.19        35.21        38.37        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MU 
       23.47        43.30        43.04        39.32        30.81        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       14.01        15.45        14.27         9.57        35.67        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       11.31         6.81        34.98        31.76        24.99        24.13 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       13.18        10.03         9.86        23.47        85.55        78.21 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 
       85.84        82.39        81.57        72.72        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ 
       63.58        49.55        66.48        16.83        19.79         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
        0.56         4.87        23.93         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 
       29.88         1.91         3.68        29.33        32.58        15.72 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O 
       36.36        37.51        36.79        27.42        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.51         1.78        24.30         2.33        22.92         1.41 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        3.95         0.26         4.27        16.31        39.29        36.62 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A2P8 TCGA-E6-A2P9 
       35.38         9.37        12.39        23.38         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U 
       16.01         7.36        16.80        31.96        35.05        27.12 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.28        32.38        34.39        19.36        35.15        12.89 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       22.26        16.34         6.21         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP 
       23.34        23.34        23.90        22.78        13.97        18.84 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 
       15.09        16.11        12.43         8.55        12.59         3.62 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       14.40        18.87        45.76        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
        6.44         2.14         3.72         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       33.99        36.00        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-KJ-A3U4 
        9.07        28.93        28.96        25.02         1.74         2.43 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.10              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           191.84            185.79 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           19.675            23.900 
[1] "0.1 - 191.8 (19.7)" "0.0 - 185.8 (23.9)"
[1] "hr=" "2"  
D16V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8Q GAIN MUTATED                                        91
  8Q GAIN WILD-TYPE                                     276
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8Q GAIN MUTATED                               8
  8Q GAIN WILD-TYPE                            12
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8Q GAIN MUTATED                                  40
  8Q GAIN WILD-TYPE                                58
D16V3, multiclass
                                         clus
vv                                        8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              91               276
  MIXED SEROUS AND ENDOMETRIOID                         8                12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    40                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    31 108
  8Q GAIN WILD-TYPE 107 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     31  108
  8Q GAIN WILD-TYPE  107  239
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               31               107
  YES             108               239
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   100   3   7  10
  8Q GAIN WILD-TYPE 236  19  10  19
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             100               236
  R1               3                19
  R2               7                10
  RX              10                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     6
  8Q GAIN WILD-TYPE                                4    13
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q GAIN MUTATED                          21
  8Q GAIN WILD-TYPE                        52
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q GAIN MUTATED                                           3   101
  8Q GAIN WILD-TYPE                                         6   254
D16V6, multiclass
                                           clus
vv                                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   6                13
  BLACK OR AFRICAN AMERICAN                              21                52
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                 101               254
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     2 103
  8Q GAIN WILD-TYPE  11 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      2  103
  8Q GAIN WILD-TYPE   11  233
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO             103               233
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    15   3
  9P GAIN WILD-TYPE 408  57
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               18               465 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                57 
$`9P GAIN MUTATED`
TCGA-A5-A1OG TCGA-AJ-A2QK TCGA-AX-A05Z TCGA-AX-A06B TCGA-AX-A2HK TCGA-AX-A3G3 
       11.44         0.39        46.45        53.92         2.96         0.03 
TCGA-B5-A11H TCGA-B5-A11I TCGA-BG-A0YV TCGA-BS-A0U9 TCGA-D1-A1NW TCGA-E6-A1M0 
       88.34        75.72        12.56        67.20         0.72        17.06 
TCGA-EO-A1Y8 TCGA-EO-A22X TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3QX 
       10.78        32.28         8.55        13.45        29.10        13.84 

$`9P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH 
       24.62        29.06        42.35        15.95         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.16         7.33        14.96         1.18         1.08         1.97 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79         0.85         2.40         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 
       13.58        19.82        29.69        68.35        72.03        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       40.50        19.36        26.33        17.75        27.32        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       38.70         0.23         0.10         0.33         0.13         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       20.52         0.13         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.13        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11J 
       11.01         4.11         8.71       185.79       113.36        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 
       11.70        11.87        15.29        12.79        62.14         5.03 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       10.22        10.16        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02         6.77         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       13.22        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        48.36         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92         7.99        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       27.12        24.79        32.38        19.40        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        12.89        27.16        26.96        22.26        16.34 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       19.27        18.84        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       12.43        15.81         6.48        19.33        12.59         3.62 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       14.40        18.87        22.82        45.76        31.04        27.35 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
        6.44        17.92         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        34.98        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       25.02        26.01        41.06         1.74        13.15         2.43 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.03              0.10 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            88.34            191.84 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           13.645            23.010 
[1] "0.0 - 88.3 (13.6)"  "0.1 - 191.8 (23.0)"
[1] "hr=" "1.5"
D17V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9P GAIN MUTATED                                        11
  9P GAIN WILD-TYPE                                     356
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9P GAIN MUTATED                               1
  9P GAIN WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9P GAIN MUTATED                                   6
  9P GAIN WILD-TYPE                                92
D17V3, multiclass
                                         clus
vv                                        9P GAIN MUTATED 9P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              11               356
  MIXED SEROUS AND ENDOMETRIOID                         1                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     6                92
[1] 3 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, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3  15
  9P GAIN WILD-TYPE 135 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3   15
  9P GAIN WILD-TYPE  135  332
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                3               135
  YES              15               332
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    11   2   1   1
  9P GAIN WILD-TYPE 325  20  16  28
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              11               325
  R1               2                20
  R2               1                16
  RX               1                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     1
  9P GAIN WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P GAIN MUTATED                           2
  9P GAIN WILD-TYPE                        71
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P GAIN MUTATED                                           1    11
  9P GAIN WILD-TYPE                                         8   344
D17V6, multiclass
                                           clus
vv                                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               2                71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  11               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"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     3   9
  9P GAIN WILD-TYPE  10 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    9
  9P GAIN WILD-TYPE   10  327
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                10
  NOT HISPANIC OR LATINO               9               327
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     6   1
  9Q GAIN WILD-TYPE 417  59
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7               476 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                59 
$`9Q GAIN MUTATED`
TCGA-A5-A1OG TCGA-AX-A3G3 TCGA-B5-A11H TCGA-BS-A0U9 TCGA-D1-A1NW TCGA-E6-A1M0 
       11.44         0.03        88.34        67.20         0.72        17.06 
TCGA-EY-A1GW 
        8.55 

$`9Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH 
       24.62        29.06        42.35        15.95         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.16         7.33        14.96         1.18         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79         0.85         2.40         3.02         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76         2.24         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26         1.28         0.92        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
        1.35        15.62         0.76         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       16.87         1.71         2.33        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89         7.86        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       36.39        11.08         4.77        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.10         0.33         0.13         0.20        20.52         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         1.18         8.35        14.47         0.13        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       17.88        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       11.87        15.29        12.79        62.14         5.03        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       10.22        10.16        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02         6.77         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       13.22        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        48.36         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92         7.99        10.78        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       33.01        27.12        32.28        24.79        32.38        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
       34.39        19.36        35.15        12.89        27.16        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       22.26        16.34         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       13.97         6.90        19.27        18.84        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       15.09        16.11        12.43        15.81         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59         3.62        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       34.98        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       96.69        59.01         9.07        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC 
       26.01        41.06         1.74        13.15         2.43        10.82 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.03              0.10 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            88.34            191.84 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           11.440            22.965 
[1] "0.0 - 88.3 (11.4)"  "0.1 - 191.8 (23.0)"
[1] "hr=" "1.4"
D18V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9Q GAIN MUTATED                                         4
  9Q GAIN WILD-TYPE                                     363
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9Q GAIN MUTATED                               1
  9Q GAIN WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9Q GAIN MUTATED                                   2
  9Q GAIN WILD-TYPE                                96
D18V3, multiclass
                                         clus
vv                                        9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               4               363
  MIXED SEROUS AND ENDOMETRIOID                         1                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     2                96
[1] 3 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, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1   6
  9Q GAIN WILD-TYPE 137 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    6
  9Q GAIN WILD-TYPE  137  341
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1               137
  YES               6               341
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED     3   1   0   1
  9Q GAIN WILD-TYPE 333  21  17  28
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               3               333
  R1               1                21
  R2               0                17
  RX               1                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     1
  9Q GAIN WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q GAIN MUTATED                           0
  9Q GAIN WILD-TYPE                        73
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q GAIN MUTATED                                           1     5
  9Q GAIN WILD-TYPE                                         8   350
D18V6, multiclass
                                           clus
vv                                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               0                73
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                   5               350
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1   4
  9Q GAIN WILD-TYPE  12 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    4
  9Q GAIN WILD-TYPE   12  332
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO               4               332
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    96  12
  10P GAIN WILD-TYPE 327  48
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               108                375 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                 48 
$`10P GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0R9 TCGA-A5-A1OG 
       37.02       105.37        28.27        20.81        24.62        11.44 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A3BI TCGA-AJ-A3EJ 
        9.60        91.04        14.96         1.97         2.24         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW 
       22.26         0.92        36.99         0.76        16.87         1.71 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LQ 
       20.91       117.99         3.39        31.73        82.52        80.78 
TCGA-AP-A1DQ TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       41.95        27.85        16.24        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A06J TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C4 
       68.35        12.26        30.02        28.54        37.78        13.28 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CJ TCGA-AX-A2HH TCGA-AX-A3FX TCGA-B5-A0JT 
       20.28        12.43        54.12        17.75         0.13        43.13 
TCGA-B5-A0JX TCGA-B5-A11F TCGA-B5-A11L TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MV 
       44.71       185.79        45.90        33.50        27.35        14.40 
TCGA-BG-A0LX TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0MG 
       20.19        20.94        35.21        34.98         7.92        48.56 
TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0W2 TCGA-BG-A187 TCGA-BG-A18A 
       30.81        15.42        24.39        56.58        14.73        14.01 
TCGA-BG-A221 TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0U7 
        1.81        35.90        10.16        16.64        46.95        30.74 
TCGA-BS-A0UV TCGA-BS-A0V7 TCGA-BS-A0WQ TCGA-D1-A0ZQ TCGA-D1-A0ZU TCGA-D1-A102 
       73.25        63.58        66.48         8.55        28.67         4.44 
TCGA-D1-A15V TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16S 
       39.48         1.91        29.33         0.66        37.32        18.67 
TCGA-D1-A17T TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A2QY 
        2.33        18.25         2.07        41.42         4.11        91.96 
TCGA-E6-A1M0 TCGA-E6-A2P9 TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 
       17.06         6.67         7.99        24.79        32.38        26.96 
TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GH TCGA-EY-A1GK TCGA-EY-A1GO 
       22.26         6.21         4.54        23.34        22.78        19.27 
TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       17.88        16.11         8.55         6.48        19.33        12.59 
TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OP TCGA-FI-A2D4 TCGA-FI-A2EW TCGA-FI-A2EX 
       14.40        45.76        31.04         7.99        59.01         9.07 

$`10P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78         3.22 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
       87.32        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        38.37        36.82        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       17.59        19.59        29.06        42.35        15.95         7.92 
TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       36.33         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        7.33         1.18         1.08         0.39        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK 
        2.40         3.02         0.49         1.12         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       14.66        22.49         1.28        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
        1.94        15.95         1.87         2.33        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        36.89         7.86        12.20        48.79       125.42 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        63.16        36.36        97.71        83.97        27.12 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05Y 
       30.90        10.42        18.25        33.73         0.56        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 
       51.09        27.39        60.66        35.01        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE 
       65.88        19.20        16.96        13.55        15.25        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       76.83        72.56        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       33.40        40.50        19.36        26.33        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       31.13        38.70         0.23         0.10         0.33         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.03         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
       14.47         0.13        80.38        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        4.11         8.71       113.36        88.34        75.72        54.44 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V 
       43.96        40.50        36.82        32.09        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       50.89        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       62.14         5.03        41.06        34.13        34.95        18.61 
TCGA-BG-A0M0 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       19.33        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        39.32        21.17        20.28 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU 
       26.66        16.34        34.29        28.54        52.83        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A222 
       12.56        13.78        15.45        15.45        14.27         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31         6.81        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
        6.21        10.22        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       10.03         9.86        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        61.87        67.99        96.49        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 
       88.34        85.84        82.39        81.57        72.72        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       62.79        49.55        63.16        16.83        19.79        29.95 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        23.93        22.55         1.74        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 
       30.08        29.88         3.68        32.58        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY 
       24.30        22.92         1.41        13.22         0.72        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       44.88         0.26         4.27        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       24.30        35.38         9.37        12.39        31.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
       48.36         2.37        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.78        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        19.36        35.15        12.89        27.16 
TCGA-EO-A3KW TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI 
       16.34        14.99         8.15        24.36        27.16        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       23.90        13.97         6.90        18.84        17.62        15.09 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.43        15.81         3.62        18.87        22.82        13.45 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       29.10        27.35        13.84         6.44        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        6.97         3.72         5.29        40.01        34.98        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 
       36.00        13.84         8.98        96.69        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       25.02        26.01        41.06         1.74        13.15         2.43 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.13               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            185.79             191.84 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             20.86              23.34 
[1] "0.1 - 185.8 (20.9)" "0.0 - 191.8 (23.3)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10P GAIN MUTATED                                        82
  10P GAIN WILD-TYPE                                     285
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10P GAIN MUTATED                               3
  10P GAIN WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10P GAIN MUTATED                                  23
  10P GAIN WILD-TYPE                                75
D19V3, multiclass
                                         clus
vv                                        10P GAIN MUTATED 10P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               82                285
  MIXED SEROUS AND ENDOMETRIOID                          3                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     23                 75
[1] 3 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, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    27  81
  10P GAIN WILD-TYPE 111 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     27   81
  10P GAIN WILD-TYPE  111  266
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                27                111
  YES               81                266
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    84   6   4   5
  10P GAIN WILD-TYPE 252  16  13  24
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               84                252
  R1                6                 16
  R2                4                 13
  RX                5                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  1     6
  10P GAIN WILD-TYPE                                3    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P GAIN MUTATED                          11
  10P GAIN WILD-TYPE                        62
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P GAIN MUTATED                                           3    83
  10P GAIN WILD-TYPE                                         6   272
D19V6, multiclass
                                           clus
vv                                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    6                 13
  BLACK OR AFRICAN AMERICAN                               11                 62
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                3                  6
  WHITE                                                   83                272
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     1  79
  10P GAIN WILD-TYPE  12 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   79
  10P GAIN WILD-TYPE   12  257
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               79                257
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    88  14
  10Q GAIN WILD-TYPE 335  46
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               102                381 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                14                 46 
$`10Q GAIN MUTATED`
TCGA-A5-A0GE TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0R9 TCGA-A5-A1OG TCGA-A5-A1OJ 
      105.37        28.27        20.81        24.62        11.44         9.60 
TCGA-A5-A2K2 TCGA-AJ-A23O TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NC 
       91.04         1.97         2.24         1.64        22.26        36.99 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LJ 
        0.76        16.87        20.91       117.99         3.39        31.73 
TCGA-AP-A0LN TCGA-AP-A0LQ TCGA-AP-A1DQ TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S 
       82.52        80.78        41.95        27.85        16.24        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A06J TCGA-AX-A0IU 
       19.82        29.69        68.35        12.26        30.02        28.54 
TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CJ TCGA-AX-A2HH 
       37.78        13.28        20.28        12.43        54.12        17.75 
TCGA-AX-A3FX TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A11F TCGA-B5-A11L TCGA-B5-A11R 
        0.13        43.13        44.71       185.79        45.90        33.50 
TCGA-B5-A11S TCGA-B5-A1MV TCGA-BG-A0LX TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M6 
       27.35        14.40        20.19        20.94        35.21         7.92 
TCGA-BG-A0MG TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0W2 TCGA-BG-A187 
       48.56        30.81        15.42        24.39        56.58        14.73 
TCGA-BG-A18A TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TI 
       14.01        35.90        10.22        16.64        46.95        61.87 
TCGA-BS-A0U7 TCGA-BS-A0UV TCGA-BS-A0V7 TCGA-BS-A0WQ TCGA-D1-A0ZQ TCGA-D1-A0ZU 
       30.74        73.25        63.58        66.48         8.55        28.67 
TCGA-D1-A15V TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16S 
       39.48         1.91        29.33         0.66        37.32        18.67 
TCGA-D1-A17T TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-DI-A2QT TCGA-E6-A1M0 
        2.33        18.25         2.07        41.42        12.39        17.06 
TCGA-E6-A2P9 TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU 
        6.67         7.99        24.79        32.38        26.96        22.26 
TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GH TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS 
        6.21         4.54        23.34        19.27        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       16.11         8.55         6.48        19.33        12.59        14.40 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-FI-A2D4 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       45.76        31.04         7.99        59.01         9.07        28.93 

$`10Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
        3.22        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0GX 
       60.53        46.55        38.37        36.82        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.96        17.59        19.59        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        7.92        36.33         8.02        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK 
        5.16         7.33        14.96         1.18         1.08         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79         0.85         2.40         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        0.76         1.68        14.66        22.49         1.28         0.92 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LE TCGA-AP-A0LG 
        7.86        12.20        48.79       125.42       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LO TCGA-AP-A0LP 
       36.36        97.71        83.97        27.12        33.40        61.64 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       31.30        35.54        49.15         6.71        30.90        10.42 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       18.25        33.73         0.56        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        53.92        51.09        27.39 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 
       60.66        35.01        43.82        40.11        65.88        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       16.96        13.55        15.25        20.05        76.83        72.56 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.23         0.10         0.33         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY 
       80.38        56.91        46.75        48.76        40.67        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        75.72        54.44        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       36.82        32.09        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW 
       17.36        16.57       191.84       102.31        50.89        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 
       11.70        11.87        15.29        12.79        62.14         5.03 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M4 
       41.06        34.13        34.95        18.61        19.33        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI 
       38.37        36.49        28.27        10.72        41.52        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV 
       43.30        43.04        39.32        21.17        20.28        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A0YV 
       16.34        34.29        28.54        52.83        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       13.78        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31         6.81        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
        6.21        10.16        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       10.03         9.86        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       77.95        67.99        96.49        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 
       85.84        82.39        81.57        72.72        59.51        62.79 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZR 
       49.55        63.16        16.83        19.79        29.95         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 
       30.08        29.88         3.68        32.58        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY 
       24.30        22.92         1.41        13.22         0.72        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27         4.11        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30        35.38         9.37        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       23.38        48.36         2.37        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.28        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       27.16        16.34        14.99         8.15        24.36        27.16 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.90        22.78        13.97         6.90        18.84 
TCGA-EY-A1GR TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM 
       17.62        12.43        15.81         3.62        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       13.45        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         3.72         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 
       33.99        36.00        13.84         8.98        96.69        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       25.02        26.01        41.06         1.74        13.15         2.43 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.13               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            185.79             191.84 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            20.925             23.210 
[1] "0.1 - 185.8 (20.9)" "0.0 - 191.8 (23.2)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10Q GAIN MUTATED                                        77
  10Q GAIN WILD-TYPE                                     290
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10Q GAIN MUTATED                               3
  10Q GAIN WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10Q GAIN MUTATED                                  22
  10Q GAIN WILD-TYPE                                76
D20V3, multiclass
                                         clus
vv                                        10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               77                290
  MIXED SEROUS AND ENDOMETRIOID                          3                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     22                 76
[1] 3 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, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    26  76
  10Q GAIN WILD-TYPE 112 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     26   76
  10Q GAIN WILD-TYPE  112  271
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                26                112
  YES               76                271
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    78   6   6   4
  10Q GAIN WILD-TYPE 258  16  11  25
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               78                258
  R1                6                 16
  R2                6                 11
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  2     6
  10Q GAIN WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q GAIN MUTATED                          12
  10Q GAIN WILD-TYPE                        61
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q GAIN MUTATED                                           3    75
  10Q GAIN WILD-TYPE                                         6   280
D20V6, multiclass
                                           clus
vv                                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         2                  2
  ASIAN                                                    6                 13
  BLACK OR AFRICAN AMERICAN                               12                 61
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                3                  6
  WHITE                                                   75                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"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3  72
  10Q GAIN WILD-TYPE  10 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3   72
  10Q GAIN WILD-TYPE   10  264
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               72                264
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    14   5
  11P GAIN WILD-TYPE 409  55
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                19                464 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 55 
$`11P GAIN MUTATED`
TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A3TW TCGA-AP-A0L8 TCGA-AX-A0IU TCGA-AX-A0IW 
        7.33         1.08         1.71        48.79        28.54        37.78 
TCGA-AX-A2H2 TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-B5-A5OE TCGA-BG-A0VT 
        4.77        43.13        17.88        50.89        34.95        24.39 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-D1-A169 TCGA-D1-A16I 
       15.45         6.81        10.22        67.20        37.32        11.51 
TCGA-DI-A1NN 
       35.38 

$`11P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.33         5.16        14.96         1.18         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79         0.85         2.40         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.33        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       12.20        20.91       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        18.25        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        35.01        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       25.12        36.39        11.08        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.10         0.33         0.13         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       80.38        56.91        46.75        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      191.84       102.31        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       15.29        12.79        62.14         5.03        41.06        34.13 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
        6.21        10.16        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N 
       36.36        37.51        36.79        27.42        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27         4.11        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10        91.96        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       27.12        32.28        24.79        32.38        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.36        35.15        12.89        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
        6.90        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59         3.62        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       34.98        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       96.69        59.01         9.07        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC 
       26.01        41.06         1.74        13.15         2.43        10.82 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.08               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             67.20             191.84 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             24.39              22.80 
[1] "1.1 - 67.2 (24.4)"  "0.0 - 191.8 (22.8)"
[1] "hr=" "2.3"
D21V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11P GAIN MUTATED                                         7
  11P GAIN WILD-TYPE                                     360
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11P GAIN MUTATED                               0
  11P GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11P GAIN MUTATED                                  12
  11P GAIN WILD-TYPE                                86
D21V3, multiclass
                                         clus
vv                                        11P GAIN MUTATED 11P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                7                360
  MIXED SEROUS AND ENDOMETRIOID                          0                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     12                 86
[1] 3 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, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     5  14
  11P GAIN WILD-TYPE 133 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5   14
  11P GAIN WILD-TYPE  133  333
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 5                133
  YES               14                333
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    11   0   1   3
  11P GAIN WILD-TYPE 325  22  16  26
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               11                325
  R1                0                 22
  R2                1                 16
  RX                3                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     0
  11P GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P GAIN MUTATED                           5
  11P GAIN WILD-TYPE                        68
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P GAIN MUTATED                                           1    12
  11P GAIN WILD-TYPE                                         8   343
D21V6, multiclass
                                           clus
vv                                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                5                 68
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   12                343
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  12
  11P GAIN WILD-TYPE  12 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   12
  11P GAIN WILD-TYPE   12  324
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               12                324
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    11   6
  11Q GAIN WILD-TYPE 412  54
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                466 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 54 
$`11Q GAIN MUTATED`
TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A2HK 
        7.33         1.08        37.78        20.28         4.77         2.96 
TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-B5-A5OE TCGA-BG-A0M2 TCGA-BG-A0VT 
       43.13        17.88        50.89        34.95        20.94        24.39 
TCGA-BG-A18C TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A1O0 TCGA-FI-A2EY 
       15.45        67.20        11.51         2.07        28.93 

$`11Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.33         5.16        14.96         1.18         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79         0.85         2.40         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.55        15.25        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 
       54.12        67.50        25.12        36.39        11.08        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.10         0.33         0.13         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.03         0.13         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
        0.13        80.38        56.91        46.75        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       23.01        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84       102.31        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       11.87        15.29        12.79        62.14         5.03        41.06 
TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 
       34.13        18.61        20.19        19.33        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       35.67        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27         4.11        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       36.62        24.30        35.38         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       91.96        23.38        48.36        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.01         7.36        16.80        10.92         7.99        10.78 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        32.28        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.38        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       27.16        26.96        22.26        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
        8.55         6.48        19.33        12.59         3.62        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        13.45        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84         6.44        17.92         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
        3.72         5.29        40.01        34.98        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ 
       28.96        25.02        26.01        41.06         1.74        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        2.43        10.82         4.21         5.52 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.08               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             67.20             191.84 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            20.280             22.965 
[1] "1.1 - 67.2 (20.3)"  "0.0 - 191.8 (23.0)"
[1] "hr=" "3.6"
D22V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11Q GAIN MUTATED                                         9
  11Q GAIN WILD-TYPE                                     358
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11Q GAIN MUTATED                               0
  11Q GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11Q GAIN MUTATED                                   8
  11Q GAIN WILD-TYPE                                90
D22V3, multiclass
                                         clus
vv                                        11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                9                358
  MIXED SEROUS AND ENDOMETRIOID                          0                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      8                 90
[1] 3 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, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     4  13
  11Q GAIN WILD-TYPE 134 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   13
  11Q GAIN WILD-TYPE  134  334
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 4                134
  YES               13                334
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED     9   1   1   2
  11Q GAIN WILD-TYPE 327  21  16  27
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                9                327
  R1                1                 21
  R2                1                 16
  RX                2                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     0
  11Q GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q GAIN MUTATED                           3
  11Q GAIN WILD-TYPE                        70
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q GAIN MUTATED                                           1    12
  11Q GAIN WILD-TYPE                                         8   343
D22V6, multiclass
                                           clus
vv                                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                3                 70
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   12                343
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  11
  11Q GAIN WILD-TYPE  13 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   11
  11Q GAIN WILD-TYPE   13  325
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               11                325
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    55   4
  12P GAIN WILD-TYPE 368  56
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                59                424 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                 56 
$`12P GAIN MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GE TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-A5-A3LP 
      149.56       105.37        17.59        11.44        46.32        14.96 
TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05P TCGA-AP-A1DO 
        1.18         0.49         0.92         0.76        20.91        31.30 
TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1CA 
       41.95        16.24        68.35        37.78        65.88        20.28 
TCGA-AX-A2HA TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A11R 
       68.71        19.36         0.03         0.13        80.38        33.50 
TCGA-B5-A11V TCGA-B5-A1N2 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0M2 TCGA-BG-A0M6 
       19.56        12.79        41.06        34.13        20.94         7.92 
TCGA-BG-A0M8 TCGA-BG-A0MG TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP 
       36.49        48.56        52.83        15.45        23.70         6.81 
TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V7 TCGA-D1-A16O TCGA-D1-A17K 
        4.80        61.87        67.20        63.58        33.63        28.08 
TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ 
        2.07        41.42        24.30        35.38        91.96        48.36 
TCGA-EO-A2CG TCGA-EO-A3AV TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GR 
       32.38        35.15        27.16         4.54        19.27        17.62 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EY 
       19.33        12.59        36.00         8.98        28.93 

$`12P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
       87.32        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        19.96        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       15.95         7.92        36.33         9.60         8.02        91.04 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A23O 
       28.64         5.33         5.16         7.33         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        0.39        19.79         0.85         2.40         3.02         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26         1.28        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       39.42        57.80        45.53        36.89         7.86        12.20 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       71.67        60.36        55.89        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       30.90        10.42        27.85        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        19.82        29.69        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       25.12        36.39        11.08         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       33.53        61.18        33.40        40.50        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.33         0.13         0.20        20.52         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18         8.35        14.47        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y 
       36.82        32.09        27.35        16.73        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A3S1 
       14.70        11.70        11.87        15.29        62.14         5.03 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 
       34.95        18.61        20.19        19.33        35.21        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK 
       38.37        28.27        10.72        41.52        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       24.39        26.66        16.34        34.29        28.54        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        35.67        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ 
       46.95        23.47        85.55        78.21        77.95        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 
       81.57        72.72        73.25        59.51        62.79        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       29.92        31.07        10.65         0.69        18.67         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
        3.52         8.48        44.88         0.26         4.27         4.11 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       16.31        39.29        36.62         9.37        12.39        31.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92         7.99        10.78        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       33.01        27.12        32.28        24.79        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       19.36        12.89        26.96        22.26        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.90        22.78        13.97         6.90        18.84        17.88 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
        3.62        14.40        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       31.04        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         3.72         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       33.99         7.99        13.84        96.69        59.01         9.07 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ 
       28.96        25.02        26.01        41.06         1.74        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        2.43        10.82         4.21         5.52 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.03               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            149.56             191.84 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             27.16              22.52 
[1] "0.0 - 149.6 (27.2)" "0.1 - 191.8 (22.5)"
[1] "hr=" "2.2"
D23V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12P GAIN MUTATED                                        32
  12P GAIN WILD-TYPE                                     335
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12P GAIN MUTATED                               3
  12P GAIN WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12P GAIN MUTATED                                  24
  12P GAIN WILD-TYPE                                74
D23V3, multiclass
                                         clus
vv                                        12P GAIN MUTATED 12P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               32                335
  MIXED SEROUS AND ENDOMETRIOID                          3                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     24                 74
[1] 3 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, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    12  47
  12P GAIN WILD-TYPE 126 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     12   47
  12P GAIN WILD-TYPE  126  300
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                12                126
  YES               47                300
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED    44   1   2   3
  12P GAIN WILD-TYPE 292  21  15  26
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               44                292
  R1                1                 21
  R2                2                 15
  RX                3                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     6
  12P GAIN WILD-TYPE                                4    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P GAIN MUTATED                          12
  12P GAIN WILD-TYPE                        61
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P GAIN MUTATED                                           2    37
  12P GAIN WILD-TYPE                                         7   318
D23V6, multiclass
                                           clus
vv                                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    6                 13
  BLACK OR AFRICAN AMERICAN                               12                 61
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   37                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"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  46
  12P GAIN WILD-TYPE  13 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   46
  12P GAIN WILD-TYPE   13  290
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               46                290
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    43   3
  12Q GAIN WILD-TYPE 380  57
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                46                437 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 57 
$`12Q GAIN MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GE TCGA-A5-A0R7 TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A3BD 
      149.56       105.37        17.59        46.32         1.18         0.49 
TCGA-AJ-A3EM TCGA-AP-A05P TCGA-AP-A1DO TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW 
       22.26        20.91        31.30        16.24        68.35        37.78 
TCGA-AX-A0J1 TCGA-AX-A1CA TCGA-AX-A2H4 TCGA-AX-A2HA TCGA-B5-A0JN TCGA-B5-A11R 
       65.88        20.28        30.12        68.71        80.38        33.50 
TCGA-B5-A11V TCGA-B5-A1N2 TCGA-B5-A5OC TCGA-BG-A0M2 TCGA-BG-A0M8 TCGA-BG-A0MG 
       19.56        12.79        41.06        20.94        36.49        48.56 
TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BS-A0TE TCGA-BS-A0U9 
       52.83        15.45        23.70         6.81         4.80        67.20 
TCGA-BS-A0V7 TCGA-D1-A16O TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-DI-A1C3 TCGA-DI-A1NN 
       63.58        33.63         2.07        41.42        24.30        35.38 
TCGA-EO-A2CG TCGA-EO-A3AV TCGA-EO-A3AZ TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1H0 
       32.38        35.15        27.16        19.27        17.62        19.33 
TCGA-EY-A210 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EY 
       12.59        36.00         8.98        28.93 

$`12Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
       87.32        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        19.96        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       91.04        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.08         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        3.02         1.12         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49         1.28         0.92        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
        1.35        15.62         0.76         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       16.87         1.71         2.33        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        12.20        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        18.25        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 
       60.66        35.01        28.54        43.82        40.11        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       19.20        16.96        13.55        15.25        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HC 
       11.08         4.77        71.24        33.53        61.18        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        8.35        14.47         0.13        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y 
       36.82        32.09        27.35        16.73        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A3S1 
       14.70        11.70        11.87        15.29        62.14         5.03 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 
       34.13        34.95        18.61        20.19        19.33        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98         7.92        38.37        28.27        10.72        41.52 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       28.54        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       20.12        11.31        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       10.16        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16Q 
       36.79        27.42        11.51        29.92        31.07        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27         4.11        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       36.62         9.37        12.39        31.10        91.96        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92         7.99        10.78        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       33.01        27.12        32.28        24.79        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       19.36        12.89        26.96        22.26        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.90        22.78        13.97         6.90        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.88        15.09        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
        6.48         3.62        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2EU TCGA-FI-A2EW 
       34.98        33.99         7.99        13.84        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
        9.07        28.96        25.02        26.01        41.06         1.74 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       13.15         2.43        10.82         4.21         5.52 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.49               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            149.56             191.84 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            29.525             22.260 
[1] "0.5 - 149.6 (29.5)" "0.0 - 191.8 (22.3)"
[1] "hr=" "2.4"
D24V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12Q GAIN MUTATED                                        30
  12Q GAIN WILD-TYPE                                     337
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12Q GAIN MUTATED                               3
  12Q GAIN WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12Q GAIN MUTATED                                  13
  12Q GAIN WILD-TYPE                                85
D24V3, multiclass
                                         clus
vv                                        12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               30                337
  MIXED SEROUS AND ENDOMETRIOID                          3                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     13                 85
[1] 3 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, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     8  38
  12Q GAIN WILD-TYPE 130 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8   38
  12Q GAIN WILD-TYPE  130  309
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 8                130
  YES               38                309
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    34   1   3   2
  12Q GAIN WILD-TYPE 302  21  14  27
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               34                302
  R1                1                 21
  R2                3                 14
  RX                2                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     5
  12Q GAIN WILD-TYPE                                4    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q GAIN MUTATED                           9
  12Q GAIN WILD-TYPE                        64
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q GAIN MUTATED                                           2    28
  12Q GAIN WILD-TYPE                                         7   327
D24V6, multiclass
                                           clus
vv                                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    5                 14
  BLACK OR AFRICAN AMERICAN                                9                 64
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   28                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"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  35
  12Q GAIN WILD-TYPE  13 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   35
  12Q GAIN WILD-TYPE   13  301
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               35                301
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    23   4
  13Q GAIN WILD-TYPE 400  56
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                27                456 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 56 
$`13Q GAIN MUTATED`
TCGA-A5-A1OG TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF 
       11.44         1.18         1.08        48.79       125.42         3.39 
TCGA-AX-A0IW TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A5OD 
       37.78        80.38        17.85        75.72       102.31        34.13 
TCGA-BK-A26L TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16S TCGA-DI-A2QY 
       24.13        39.48         0.66        11.51        18.67        91.96 
TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EY-A1GO TCGA-EY-A210 
       10.92        24.79        32.38        26.96        19.27        12.59 
TCGA-EY-A214 TCGA-EY-A54A TCGA-FI-A2F9 
       14.40         3.72        26.01 

$`13Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH 
       24.62        29.06        42.35        15.95         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.16         7.33        14.96         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.85         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        2.24         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
        1.28         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
        0.76         1.94        15.95         1.87        16.87         1.71 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.33        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       12.20        20.91       117.99       110.37        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       33.73         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        28.54        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       36.39        11.08         4.77        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.10         0.33         0.13         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       12.79        62.14         5.03        41.06        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        35.67        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 
       29.88         1.91         3.68        29.33        32.58        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       29.92        31.07        33.63        10.65         0.69         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       24.30        35.38         9.37        12.39        31.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       27.12        32.28        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        22.26        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.90        22.78        13.97         6.90        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        15.09        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
        6.48        19.33         3.62        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
       17.92         2.14         6.97         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV 
       59.01         9.07        28.93        28.96        25.02        41.06 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74        13.15         2.43        10.82         4.21         5.52 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.66               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            125.42             191.84 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             24.13              22.80 
[1] "0.7 - 125.4 (24.1)" "0.0 - 191.8 (22.8)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  13Q GAIN MUTATED                                         8
  13Q GAIN WILD-TYPE                                     359
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  13Q GAIN MUTATED                               1
  13Q GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  13Q GAIN MUTATED                                  18
  13Q GAIN WILD-TYPE                                80
D25V3, multiclass
                                         clus
vv                                        13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                8                359
  MIXED SEROUS AND ENDOMETRIOID                          1                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     18                 80
[1] 3 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, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     8  19
  13Q GAIN WILD-TYPE 130 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      8   19
  13Q GAIN WILD-TYPE  130  328
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 8                130
  YES               19                328
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED    17   0   2   3
  13Q GAIN WILD-TYPE 319  22  15  26
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               17                319
  R1                0                 22
  R2                2                 15
  RX                3                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     2
  13Q GAIN WILD-TYPE                                4    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q GAIN MUTATED                           6
  13Q GAIN WILD-TYPE                        67
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q GAIN MUTATED                                           0    16
  13Q GAIN WILD-TYPE                                         9   339
D25V6, multiclass
                                           clus
vv                                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                                6                 67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   16                339
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  15
  13Q GAIN WILD-TYPE  13 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   15
  13Q GAIN WILD-TYPE   13  321
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               15                321
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    30   6
  14Q GAIN WILD-TYPE 393  54
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                447 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 6                 54 
$`14Q GAIN MUTATED`
TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A3EM TCGA-AJ-A3IA 
       36.33         8.02        91.04        14.96        22.26         0.92 
TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A3K1 TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H4 
        1.35         1.71        18.25        12.43        11.08        30.12 
TCGA-B5-A0JR TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A26L 
       56.91        17.88        50.89         6.81        35.90        24.13 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A169 TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-DI-A2QY 
       16.64        67.20        37.32         2.07        41.42        91.96 
TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GW 
       17.06        10.92        24.79        26.96         4.54         8.55 
TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-K6-A3WQ 
        6.44        36.00        59.01         9.07        28.93        13.15 

$`14Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        9.60        46.32        28.64         5.33         5.16         7.33 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        1.18         1.08         1.97         0.39        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40         3.02         0.49         1.12         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.68         1.64        14.66        22.49         1.28        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        15.62         0.76         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       16.87         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        33.73         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.55        15.25        20.28        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H5 
       54.12        67.50        25.12        36.39         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.10         0.33         0.13         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.03         0.13         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.13        80.38        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       23.01        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84       102.31        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       11.87        15.29        12.79        62.14         5.03        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       20.12        11.31        34.98         6.21        10.22        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.76        24.99        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95         3.52         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       24.30        35.38         9.37        12.39        31.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       48.36         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       32.28        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        22.26        16.34         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        15.09        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       19.33        12.59         3.62        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       13.45        45.76        31.04        29.10        27.35        13.84 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       34.98        33.99         7.99        13.84         8.98        96.69 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 
       28.96        25.02        26.01        41.06         1.74         2.43 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.92               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             91.96             191.84 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            18.065             23.010 
[1] "0.9 - 92.0 (18.1)"  "0.0 - 191.8 (23.0)"
[1] "hr=" "1.5"
D26V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  14Q GAIN MUTATED                                        14
  14Q GAIN WILD-TYPE                                     353
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  14Q GAIN MUTATED                               2
  14Q GAIN WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  14Q GAIN MUTATED                                  20
  14Q GAIN WILD-TYPE                                78
D26V3, multiclass
                                         clus
vv                                        14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               14                353
  MIXED SEROUS AND ENDOMETRIOID                          2                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     20                 78
[1] 3 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, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     3  33
  14Q GAIN WILD-TYPE 135 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3   33
  14Q GAIN WILD-TYPE  135  314
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 3                135
  YES               33                314
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    24   2   1   5
  14Q GAIN WILD-TYPE 312  20  16  24
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               24                312
  R1                2                 20
  R2                1                 16
  RX                5                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     0
  14Q GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q GAIN MUTATED                           3
  14Q GAIN WILD-TYPE                        70
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q GAIN MUTATED                                           1    28
  14Q GAIN WILD-TYPE                                         8   327
D26V6, multiclass
                                           clus
vv                                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                3                 70
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   28                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"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1  26
  14Q GAIN WILD-TYPE  12 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1   26
  14Q GAIN WILD-TYPE   12  310
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               26                310
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     6   3
  15Q GAIN WILD-TYPE 417  57
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                474 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 57 
$`15Q GAIN MUTATED`
TCGA-AJ-A3IA TCGA-AX-A3G1 TCGA-B5-A11I TCGA-BS-A0TE TCGA-D1-A102 TCGA-DI-A1NN 
        0.92        20.52        75.72         4.80         4.44        35.38 
TCGA-E6-A1M0 TCGA-EY-A1GW TCGA-PG-A5BC 
       17.06         8.55        10.82 

$`15Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        0.49         1.12         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26         1.28        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
        1.35        15.62         0.76         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       16.87         1.71         2.33        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89         7.86        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       36.39        11.08         4.77        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.10         0.33         0.13         0.20         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         1.18         8.35        14.47         0.13        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       17.88        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       11.87        15.29        12.79        62.14         5.03        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       10.22        10.16        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       24.30         9.37        12.39        31.10        91.96        23.38 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       48.36         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       27.12        32.28        24.79        32.38        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.36        35.15        12.89        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
        6.90        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        15.81         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
        3.62        14.40        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       31.04        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         3.72         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        26.01 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-QS-A5YQ TCGA-QS-A5YR 
       41.06         1.74        13.15         2.43         4.21         5.52 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.92               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             75.72             191.84 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             10.82              23.11 
[1] "0.9 - 75.7 (10.8)"  "0.0 - 191.8 (23.1)"
[1] "hr=" "4.1"
D27V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  15Q GAIN MUTATED                                         6
  15Q GAIN WILD-TYPE                                     361
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  15Q GAIN MUTATED                               0
  15Q GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  15Q GAIN MUTATED                                   3
  15Q GAIN WILD-TYPE                                95
D27V3, multiclass
                                         clus
vv                                        15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                6                361
  MIXED SEROUS AND ENDOMETRIOID                          0                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      3                 95
[1] 3 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, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1   8
  15Q GAIN WILD-TYPE 137 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    8
  15Q GAIN WILD-TYPE  137  339
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 1                137
  YES                8                339
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     3   1   1   1
  15Q GAIN WILD-TYPE 333  21  16  28
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                3                333
  R1                1                 21
  R2                1                 16
  RX                1                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     1
  15Q GAIN WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q GAIN MUTATED                           2
  15Q GAIN WILD-TYPE                        71
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q GAIN MUTATED                                           0     6
  15Q GAIN WILD-TYPE                                         9   349
D27V6, multiclass
                                           clus
vv                                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                2                 71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                    6                349
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1   7
  15Q GAIN WILD-TYPE  12 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    7
  15Q GAIN WILD-TYPE   12  329
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO                7                329
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    21   2
  16P GAIN WILD-TYPE 402  58
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                460 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 58 
$`16P GAIN MUTATED`
TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A3G1 TCGA-B5-A11G 
       91.04        14.96        37.78        13.55        20.52       113.36 
TCGA-B5-A11V TCGA-B5-A1N2 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BK-A26L TCGA-BS-A0U9 
       19.56        12.79        36.49        24.39        24.13        67.20 
TCGA-D1-A102 TCGA-D1-A168 TCGA-EO-A1Y7 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
        4.44        36.10         7.99        22.26        16.34         4.54 
TCGA-EY-A1GW TCGA-EY-A547 TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EW 
        8.55        17.92         3.72        36.00        59.01 

$`16P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33         9.60         8.02        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33         1.18         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79         0.85         2.40         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         0.03         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       14.47         0.13        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H 
       17.85        11.01         4.11         8.71       185.79        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y 
       32.09        33.50        27.35        16.73        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A3S1 
       14.70        11.70        11.87        15.29        62.14         5.03 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.94        35.21        34.98         7.92        38.37        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       39.32        30.81        21.17        20.28        15.42        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31         6.81        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.16        31.76        24.99        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       12.39        31.10        91.96        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.78        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       24.79        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       12.89        27.16        26.96         6.21        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       13.97         6.90        19.27        18.84        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       15.09        16.11        12.43        15.81         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59         3.62        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84         6.44 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        2.14         6.97         5.29        40.01        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        13.84         8.98        96.69         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ 
       28.96        25.02        26.01        41.06         1.74        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        2.43        10.82         4.21         5.52 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3.72               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            113.36             191.84 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            20.520             22.965 
[1] "3.7 - 113.4 (20.5)" "0.0 - 191.8 (23.0)"
[1] "hr=" "1.5"
D28V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16P GAIN MUTATED                                        13
  16P GAIN WILD-TYPE                                     354
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16P GAIN MUTATED                               1
  16P GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16P GAIN MUTATED                                   9
  16P GAIN WILD-TYPE                                89
D28V3, multiclass
                                         clus
vv                                        16P GAIN MUTATED 16P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               13                354
  MIXED SEROUS AND ENDOMETRIOID                          1                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      9                 89
[1] 3 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, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     3  20
  16P GAIN WILD-TYPE 135 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3   20
  16P GAIN WILD-TYPE  135  327
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 3                135
  YES               20                327
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    14   2   0   3
  16P GAIN WILD-TYPE 322  20  17  26
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               14                322
  R1                2                 20
  R2                0                 17
  RX                3                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     0
  16P GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P GAIN MUTATED                           6
  16P GAIN WILD-TYPE                        67
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P GAIN MUTATED                                           1    13
  16P GAIN WILD-TYPE                                         8   342
D28V6, multiclass
                                           clus
vv                                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                6                 67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   13                342
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  15
  16P GAIN WILD-TYPE  12 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   15
  16P GAIN WILD-TYPE   12  321
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               15                321
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     8   1
  16Q GAIN WILD-TYPE 415  59
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 9                474 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 59 
$`16Q GAIN MUTATED`
TCGA-AX-A1C8 TCGA-AX-A2HH TCGA-B5-A0JN TCGA-B5-A11V TCGA-BK-A26L TCGA-BS-A0U9 
       13.55        17.75        80.38        19.56        24.13        67.20 
TCGA-EY-A1GW TCGA-EY-A54A TCGA-FI-A2D2 
        8.55         3.72        36.00 

$`16Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        0.49         1.12         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26         1.28         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65         1.35        15.62         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
        1.87        16.87         1.71         2.33        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89         7.86        12.20        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       33.73         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       13.28        19.20        16.96        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       36.39        11.08         4.77        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.33         0.13         0.20        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.23         1.18         8.35        14.47         0.13        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       16.73        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       15.29        12.79        62.14         5.03        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98         7.92        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31         6.81        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.16        31.76        24.99        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27         4.11        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       35.38         9.37        12.39        31.10        91.96        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92         7.99        10.78        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       33.01        27.12        32.28        24.79        32.38        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
       34.39        19.36        35.15        12.89        27.16        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       22.26        16.34         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       13.97         6.90        19.27        18.84        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       15.09        16.11        12.43        15.81         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59         3.62        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
       17.92         2.14         6.97         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       33.99         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
        9.07        28.93        28.96        25.02        26.01        41.06 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74        13.15         2.43        10.82         4.21         5.52 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3.72               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             80.38             191.84 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             19.56              22.87 
[1] "3.7 - 80.4 (19.6)"  "0.0 - 191.8 (22.9)"
[1] "hr=" "1.1"
D29V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16Q GAIN MUTATED                                         5
  16Q GAIN WILD-TYPE                                     362
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16Q GAIN MUTATED                               1
  16Q GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16Q GAIN MUTATED                                   3
  16Q GAIN WILD-TYPE                                95
D29V3, multiclass
                                         clus
vv                                        16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                5                362
  MIXED SEROUS AND ENDOMETRIOID                          1                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      3                 95
[1] 3 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, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1   8
  16Q GAIN WILD-TYPE 137 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    8
  16Q GAIN WILD-TYPE  137  339
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 1                137
  YES                8                339
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED     2   3   0   2
  16Q GAIN WILD-TYPE 334  19  17  27
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                2                334
  R1                3                 19
  R2                0                 17
  RX                2                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     0
  16Q GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q GAIN MUTATED                           3
  16Q GAIN WILD-TYPE                        70
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q GAIN MUTATED                                           1     5
  16Q GAIN WILD-TYPE                                         8   350
D29V6, multiclass
                                           clus
vv                                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                3                 70
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                    5                350
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1   6
  16Q GAIN WILD-TYPE  12 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    6
  16Q GAIN WILD-TYPE   12  330
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO                6                330
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    10   1
  17P GAIN WILD-TYPE 413  59
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                11                472 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 59 
$`17P GAIN MUTATED`
TCGA-A5-A0R7 TCGA-AJ-A3IA TCGA-AX-A1C4 TCGA-AX-A2HK TCGA-BG-A0M4 TCGA-BK-A0CC 
       17.59         0.92        13.28         2.96        34.98        10.22 
TCGA-D1-A1O0 TCGA-DI-A2QY TCGA-EO-A3B1 TCGA-EY-A1GO TCGA-K6-A3WQ 
        2.07        91.96        26.96        19.27        13.15 

$`17P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        23.21        68.65        19.96        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.16         7.33        14.96         1.18         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79         0.85         2.40         3.02         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76         2.24         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26         1.28        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C7 
       37.78        43.82        40.11        65.88        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       15.29        12.79        62.14         5.03        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
        6.81        35.90        34.98         6.21        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
        4.11        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
        9.37        12.39        31.10        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       32.28        24.79        32.38        19.40        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       35.15        12.89        27.16        22.26        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.90        22.78        13.97         6.90        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
        8.55         6.48        19.33        12.59         3.62        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        13.45        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84         6.44        17.92         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
        3.72         5.29        40.01        34.98        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
       28.93        28.96        25.02        26.01        41.06         1.74 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        2.43        10.82         4.21         5.52 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.92               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             91.96             191.84 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             13.28              23.11 
[1] "0.9 - 92.0 (13.3)"  "0.0 - 191.8 (23.1)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17P GAIN MUTATED                                         6
  17P GAIN WILD-TYPE                                     361
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17P GAIN MUTATED                               0
  17P GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17P GAIN MUTATED                                   5
  17P GAIN WILD-TYPE                                93
D30V3, multiclass
                                         clus
vv                                        17P GAIN MUTATED 17P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                6                361
  MIXED SEROUS AND ENDOMETRIOID                          0                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      5                 93
[1] 3 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, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     3   8
  17P GAIN WILD-TYPE 135 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    8
  17P GAIN WILD-TYPE  135  339
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 3                135
  YES                8                339
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     7   1   0   2
  17P GAIN WILD-TYPE 329  21  17  27
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                7                329
  R1                1                 21
  R2                0                 17
  RX                2                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     0
  17P GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P GAIN MUTATED                           1
  17P GAIN WILD-TYPE                        72
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P GAIN MUTATED                                           0     9
  17P GAIN WILD-TYPE                                         9   346
D30V6, multiclass
                                           clus
vv                                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                1                 72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                    9                346
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1   8
  17P GAIN WILD-TYPE  12 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    8
  17P GAIN WILD-TYPE   12  328
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO                8                328
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    19   6
  17Q GAIN WILD-TYPE 404  54
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                25                458 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                 54 
$`17Q GAIN MUTATED`
TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-AJ-A3IA TCGA-AJ-A3QS TCGA-AX-A1C4 TCGA-AX-A1CF 
       36.82        17.59         0.92        16.87        13.28        76.83 
TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MY TCGA-BG-A0M2 
        4.77         2.96         4.11        75.72        11.87        20.94 
TCGA-BG-A0M4 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-D1-A1O0 TCGA-DI-A1NN TCGA-EO-A2CH 
       34.98         6.81        10.22         2.07        35.38        19.40 
TCGA-EO-A3B1 TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A4KR 
       26.96        19.27        15.09        13.45        27.35         6.44 
TCGA-K6-A3WQ 
       13.15 

$`17Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        19.96        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       42.35        15.95         7.92        11.44        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        7.33        14.96         1.18         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79         0.85         2.40         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26         1.28        36.99        20.65         1.35        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW 
        0.76         1.94        15.95         1.87         1.71         2.33 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       39.42        57.80        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        18.25        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        65.88        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       20.28        12.43        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       25.12        36.39        11.08        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        27.32        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.33         0.13         0.20        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         1.18         8.35        14.47         0.13        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       12.79        62.14         5.03        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0M7 
       18.61        20.19        19.33        35.21         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
        6.21        10.16        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        67.20        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27         4.11        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30         9.37        12.39        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92         7.99        10.78        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       35.05        33.01        27.12        32.28        24.79        32.38 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU 
       34.39        19.36        35.15        12.89        27.16        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU 
        6.90        18.84        17.88        17.62        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       15.81         8.55         6.48        19.33        12.59         3.62 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       14.40        18.87        22.82        45.76        31.04        29.10 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       13.84        17.92         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        34.98        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC 
       25.02        26.01        41.06         1.74         2.43        10.82 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.92               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             76.83             191.84 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             15.09              23.34 
[1] "0.9 - 76.8 (15.1)"  "0.0 - 191.8 (23.3)"
[1] "hr=" "2.9"
D31V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17Q GAIN MUTATED                                        11
  17Q GAIN WILD-TYPE                                     356
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17Q GAIN MUTATED                               0
  17Q GAIN WILD-TYPE                            20
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17Q GAIN MUTATED                                  14
  17Q GAIN WILD-TYPE                                84
D31V3, multiclass
                                         clus
vv                                        17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               11                356
  MIXED SEROUS AND ENDOMETRIOID                          0                 20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     14                 84
[1] 3 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, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     7  18
  17Q GAIN WILD-TYPE 131 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7   18
  17Q GAIN WILD-TYPE  131  329
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 7                131
  YES               18                329
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED    14   1   4   2
  17Q GAIN WILD-TYPE 322  21  13  27
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               14                322
  R1                1                 21
  R2                4                 13
  RX                2                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     0
  17Q GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q GAIN MUTATED                          11
  17Q GAIN WILD-TYPE                        62
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q GAIN MUTATED                                           0    12
  17Q GAIN WILD-TYPE                                         9   343
D31V6, multiclass
                                           clus
vv                                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                               11                 62
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   12                343
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     1  18
  17Q GAIN WILD-TYPE  12 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1   18
  17Q GAIN WILD-TYPE   12  318
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               18                318
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    50  12
  18P GAIN WILD-TYPE 373  48
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                62                421 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                 48 
$`18P GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH 
       37.02       105.37        36.82        19.96        11.44        36.33 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH 
        1.08         0.49        22.26         0.92         1.35         0.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A053 TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF 
       16.87         1.71         5.95        48.79       125.42         3.39 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A1CA 
       97.71        33.40        41.95        18.25        33.73        20.28 
TCGA-AX-A2H4 TCGA-AX-A2HC TCGA-AX-A2HK TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11I 
       30.12        33.40         2.96         0.13        17.85        75.72 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT 
        5.03        34.13        34.95         7.92        36.49        24.39 
TCGA-BG-A2AE TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A169 
       23.70        10.22        24.13        67.20        39.48        37.32 
TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
        3.52        44.88         4.11        35.38         9.37        91.96 
TCGA-E6-A1LZ TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1GR TCGA-EY-A210 
       48.36        19.40        27.16        22.26        17.62        12.59 
TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-FI-A2CY TCGA-FI-A2F9 TCGA-K6-A3WQ 
        3.62        13.45        27.35        34.98        26.01        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC 
        2.43        10.82 

$`18P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78         3.22 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
       87.32        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
        7.92         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O 
        5.33         5.16         7.33        14.96         1.18         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        0.39        19.79         0.85         2.40         3.02         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
        1.28        36.99        20.65        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
        1.87         2.33        83.67        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       12.20        20.91       117.99       110.37        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       31.30        35.54        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        16.24         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 
       25.12        36.39        11.08         4.77        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       61.18        68.71        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       27.32        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.13         0.20        20.52         0.03         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18         8.35        14.47        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       88.34        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       62.14        41.06        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        34.98        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
        9.57        35.67        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       34.98         6.21        10.16        31.76        24.99        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        21.99        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH 
        3.95        41.42         8.48         0.26         4.27        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       39.29        36.62        24.30        12.39        31.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU 
       27.12        32.28        24.79        32.38        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       35.15        12.89        26.96        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.88        15.09        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
        6.48        19.33        14.40        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       31.04        29.10        13.84         6.44        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 
        6.97         3.72         5.29        40.01        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-QS-A5YQ 
       28.93        28.96        25.02        41.06         1.74         4.21 
TCGA-QS-A5YR 
        5.52 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.13               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            125.42             191.84 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             22.26              22.92 
[1] "0.1 - 125.4 (22.3)" "0.0 - 191.8 (22.9)"
[1] "hr=" "1.8"
D32V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18P GAIN MUTATED                                        18
  18P GAIN WILD-TYPE                                     349
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18P GAIN MUTATED                               5
  18P GAIN WILD-TYPE                            15
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18P GAIN MUTATED                                  39
  18P GAIN WILD-TYPE                                59
D32V3, multiclass
                                         clus
vv                                        18P GAIN MUTATED 18P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               18                349
  MIXED SEROUS AND ENDOMETRIOID                          5                 15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     39                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V4, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    14  48
  18P GAIN WILD-TYPE 124 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     14   48
  18P GAIN WILD-TYPE  124  299
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                14                124
  YES               48                299
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED    39   1   6   7
  18P GAIN WILD-TYPE 297  21  11  22
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               39                297
  R1                1                 21
  R2                6                 11
  RX                7                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     2
  18P GAIN WILD-TYPE                                4    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P GAIN MUTATED                          21
  18P GAIN WILD-TYPE                        52
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P GAIN MUTATED                                           1    34
  18P GAIN WILD-TYPE                                         8   321
D32V6, multiclass
                                           clus
vv                                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                               21                 52
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   34                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"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  41
  18P GAIN WILD-TYPE  11 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   41
  18P GAIN WILD-TYPE   11  295
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               41                295
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    29   9
  18Q GAIN WILD-TYPE 394  51
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                38                445 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                 51 
$`18Q GAIN MUTATED`
TCGA-A5-A0GE TCGA-A5-A0R6 TCGA-AJ-A23N TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF 
      105.37        19.96         1.08        22.26         0.92         1.35 
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LO 
        0.76         5.95        48.79       125.42         3.39        33.40 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A2HC TCGA-AX-A2HK TCGA-B5-A11I TCGA-B5-A3S1 
       18.25        33.73        33.40         2.96        75.72         5.03 
TCGA-B5-A5OD TCGA-BG-A0VT TCGA-BG-A2AE TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A15V 
       34.13        24.39        23.70        24.13        67.20        39.48 
TCGA-D1-A16I TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-EO-A2CH 
       11.51         3.52        44.88        35.38         9.37        19.40 
TCGA-EO-A3AZ TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-FI-A2F9 
       27.16        17.62        12.59        27.35         6.44        26.01 
TCGA-K6-A3WQ TCGA-KJ-A3U4 
       13.15         2.43 

$`18Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
        3.22        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       42.35        15.95         7.92        11.44        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33        14.96         1.18         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.85         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
        2.24         1.68         1.64        14.66        22.49         1.28 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       16.87         1.71         2.33        83.67        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
        7.86        12.20        20.91       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO 
        6.71        30.90        10.42        27.85        16.24         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       68.71        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       12.79        62.14        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
       10.22        10.16        31.76        24.99        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         1.41         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02         6.77         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH 
       41.42         8.48         0.26         4.27         4.11        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       39.29        36.62        24.30        12.39        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92         7.99        10.78        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       35.05        33.01        27.12        32.28        24.79        32.38 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU 
       34.39        19.36        35.15        12.89        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT 
        6.90        19.27        18.84        17.88        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 
       12.43        15.81         8.55         6.48        19.33         3.62 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        13.45        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       29.10        13.84        17.92         2.14         6.97         3.72 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.29        40.01        34.98        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-PG-A5BC TCGA-QS-A5YQ 
       28.96        25.02        41.06         1.74        10.82         4.21 
TCGA-QS-A5YR 
        5.52 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.76               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            125.42             191.84 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             21.11              22.92 
[1] "0.8 - 125.4 (21.1)" "0.0 - 191.8 (22.9)"
[1] "hr=" "2.3"
D33V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18Q GAIN MUTATED                                        14
  18Q GAIN WILD-TYPE                                     353
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18Q GAIN MUTATED                               4
  18Q GAIN WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18Q GAIN MUTATED                                  20
  18Q GAIN WILD-TYPE                                78
D33V3, multiclass
                                         clus
vv                                        18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               14                353
  MIXED SEROUS AND ENDOMETRIOID                          4                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     20                 78
[1] 3 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, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     9  29
  18Q GAIN WILD-TYPE 129 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      9   29
  18Q GAIN WILD-TYPE  129  318
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 9                129
  YES               29                318
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    24   0   3   6
  18Q GAIN WILD-TYPE 312  22  14  23
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               24                312
  R1                0                 22
  R2                3                 14
  RX                6                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     1
  18Q GAIN WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q GAIN MUTATED                          10
  18Q GAIN WILD-TYPE                        63
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q GAIN MUTATED                                           1    23
  18Q GAIN WILD-TYPE                                         8   332
D33V6, multiclass
                                           clus
vv                                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                               10                 63
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   23                332
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1  25
  18Q GAIN WILD-TYPE  12 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1   25
  18Q GAIN WILD-TYPE   12  311
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               25                311
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    36   9
  19P GAIN WILD-TYPE 387  51
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                45                438 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 9                 51 
$`19P GAIN MUTATED`
TCGA-AJ-A3BI TCGA-AJ-A3IA TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI 
        2.24         0.92        48.79       125.42         3.39        97.71 
TCGA-AP-A1DQ TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CR TCGA-AX-A2H2 
       41.95        37.78        16.96        13.55        11.08         4.77 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A3G1 TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A1MY 
       33.53        61.18        20.52        80.38        17.85        11.87 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A0VT TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0V8 
       12.79         5.03        24.39        10.22        16.64        49.55 
TCGA-D1-A0ZZ TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH 
       22.55        18.67        18.25         2.07        44.88         4.11 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CG 
        9.37        31.10        91.96        10.92        24.79        32.38 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A212 
       22.26        16.34        23.90        17.62        12.59         3.62 
TCGA-EY-A2OQ TCGA-EY-A547 TCGA-FI-A2F9 
       29.10        17.92        26.01 

$`19P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        0.49         1.12         0.76         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26         1.28        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
        7.86        12.20        20.91       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 
       54.12        67.50        25.12        36.39        30.12        71.24 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.33         0.13         0.20         0.03         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18         8.35        14.47         0.13        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FC 
       50.89        14.40        14.70        11.70        15.29        62.14 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       10.16        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        62.79        63.58        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22         0.72        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        0.26         4.27        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       35.38        12.39        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
        6.67        16.01         7.36        16.80         7.99        10.78 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH 
       31.96        35.05        33.01        27.12        32.28        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
       34.39        19.36        35.15        12.89        27.16        26.96 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.34        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.88        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
        8.55         6.48        19.33        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       13.45        45.76        31.04        27.35        13.84         6.44 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         3.72         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV 
       59.01         9.07        28.93        28.96        25.02        41.06 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74        13.15         2.43        10.82         4.21         5.52 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.92               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            125.42             191.84 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            18.250             23.325 
[1] "0.9 - 125.4 (18.2)" "0.0 - 191.8 (23.3)"
[1] "hr=" "1.8"
D34V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19P GAIN MUTATED                                        18
  19P GAIN WILD-TYPE                                     349
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19P GAIN MUTATED                               3
  19P GAIN WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19P GAIN MUTATED                                  24
  19P GAIN WILD-TYPE                                74
D34V3, multiclass
                                         clus
vv                                        19P GAIN MUTATED 19P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               18                349
  MIXED SEROUS AND ENDOMETRIOID                          3                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     24                 74
[1] 3 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, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    10  35
  19P GAIN WILD-TYPE 128 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     10   35
  19P GAIN WILD-TYPE  128  312
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                10                128
  YES               35                312
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    30   3   2   4
  19P GAIN WILD-TYPE 306  19  15  25
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               30                306
  R1                3                 19
  R2                2                 15
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     1
  19P GAIN WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P GAIN MUTATED                          13
  19P GAIN WILD-TYPE                        60
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P GAIN MUTATED                                           1    26
  19P GAIN WILD-TYPE                                         8   329
D34V6, multiclass
                                           clus
vv                                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                               13                 60
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   26                329
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  31
  19P GAIN WILD-TYPE  12 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   31
  19P GAIN WILD-TYPE   12  305
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               31                305
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    37  10
  19Q GAIN WILD-TYPE 386  50
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                47                436 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                 50 
$`19Q GAIN MUTATED`
TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0L8 
       11.44        46.32        14.96         0.92         0.76        48.79 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 
       97.71        41.95        28.54        37.78        16.96        13.55 
TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A3G1 TCGA-B5-A0JN 
       20.28        11.08         4.77        33.53        20.52        80.38 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A0M6 TCGA-BG-A0VT TCGA-BK-A26L 
       11.87        12.79         5.03         7.92        24.39        24.13 
TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A1O0 
       16.64        22.55        39.48        18.67        18.25         2.07 
TCGA-D1-A2G7 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 
       44.88         9.37        31.10        91.96        48.36        10.92 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A210 
       24.79        32.38        22.26        17.62        15.09        12.59 
TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A547 TCGA-FI-A2F9 TCGA-PG-A5BC 
        3.62        29.10        17.92        26.01        10.82 

$`19Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH 
       24.62        29.06        42.35        15.95         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        91.04        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33         1.18         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.85         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        2.24         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
        1.28        36.99        20.65         1.35        15.62         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 
       15.95         1.87        16.87         1.71         2.33        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89         7.86        12.20        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       51.09        27.39        30.02        60.66        35.01        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CC 
       40.11        65.88        13.28        19.20        15.25        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       36.39        30.12        71.24        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         0.03         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.13        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A5OC 
       14.40        14.70        11.70        15.29        62.14        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        21.17        20.28        15.42        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        35.90        34.98         6.21        10.22        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.76        24.99        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74         4.44        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02         6.77         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
       13.22         0.72        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52        41.42         8.48         0.26         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
        4.11        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       12.39        23.38        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80         7.99        10.78        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       33.01        27.12        32.28        19.40        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 
       35.15        12.89        27.16        26.96        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        17.88        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
        6.48        19.33        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       45.76        31.04        27.35        13.84         6.44         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        6.97         3.72         5.29        40.01        34.98        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       36.00         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-H5-A2HR 
        9.07        28.93        28.96        25.02        41.06         1.74 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-QS-A5YQ TCGA-QS-A5YR 
       13.15         2.43         4.21         5.52 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.76               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             97.71             191.84 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            18.670             23.325 
[1] "0.8 - 97.7 (18.7)"  "0.0 - 191.8 (23.3)"
[1] "hr=" "2.1"
D35V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19Q GAIN MUTATED                                        12
  19Q GAIN WILD-TYPE                                     355
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19Q GAIN MUTATED                               3
  19Q GAIN WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19Q GAIN MUTATED                                  32
  19Q GAIN WILD-TYPE                                66
D35V3, multiclass
                                         clus
vv                                        19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               12                355
  MIXED SEROUS AND ENDOMETRIOID                          3                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     32                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    13  34
  19Q GAIN WILD-TYPE 125 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     13   34
  19Q GAIN WILD-TYPE  125  313
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                13                125
  YES               34                313
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    32   3   2   4
  19Q GAIN WILD-TYPE 304  19  15  25
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               32                304
  R1                3                 19
  R2                2                 15
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     2
  19Q GAIN WILD-TYPE                                4    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q GAIN MUTATED                          16
  19Q GAIN WILD-TYPE                        57
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q GAIN MUTATED                                           0    26
  19Q GAIN WILD-TYPE                                         9   329
D35V6, multiclass
                                           clus
vv                                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                               16                 57
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   26                329
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0  37
  19Q GAIN WILD-TYPE  13 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   37
  19Q GAIN WILD-TYPE   13  299
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               37                299
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    79  17
  20P GAIN WILD-TYPE 344  43
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                96                387 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                17                 43 
$`20P GAIN MUTATED`
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       11.44        36.33        46.32        28.64         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
        1.18         1.08         2.40         2.24         1.64        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A1DO 
        0.92         0.76        57.80       125.42         3.39        31.30 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       41.95        18.25        53.92        28.54        37.78        16.96 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK 
       20.28        12.43        11.08         4.77        30.12         2.96 
TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3GI 
        0.23         0.13         0.20         0.03         0.23         0.13 
TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11V 
       80.38        43.13         4.11        75.72        45.90        19.56 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0MS 
      102.31        11.87        12.79         5.03        34.13        30.81 
TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A26L 
       24.39        52.83        15.45         1.81        10.22        24.13 
TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A102 
       13.18         4.80        67.20        72.72        49.55         4.44 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW 
       37.32        11.51        29.92        31.07        18.67         0.72 
TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QT TCGA-EO-A1Y5 
        2.07        41.42         4.11        35.38        12.39        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AV 
        7.99        10.78        24.79        32.38        19.40        35.15 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GM TCGA-EY-A1GR 
       26.96        22.26        16.34         6.21         6.90        17.62 
TCGA-EY-A1GS TCGA-EY-A214 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 
       15.09        14.40        29.10        27.35         6.44        17.92 
TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-K6-A3WQ 
        3.72        40.01        59.01         9.07        28.93        13.15 

$`20P GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ 
       24.62        29.06        42.35        15.95         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QK 
        8.02        91.04         5.33         5.16         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         0.85         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.68        14.66        22.49         1.28        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
        1.35        15.62         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        39.42        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.20        20.91        48.79       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       71.67        60.36        55.89        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO 
       30.90        10.42        27.85        16.24        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 
       27.39        30.02        60.66        35.01        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE 
       65.88        13.28        19.20        13.55        15.25        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.10         0.33        20.52         0.13         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47        56.91        46.75        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O 
      185.79       113.36        88.34        54.44        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W 
       36.82        32.09        33.50        27.35        16.73        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV 
       18.41        17.36        16.57       191.84        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OE 
       14.70        11.70        15.29        62.14        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        39.32        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        26.66        16.34        34.29        28.54 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        14.27         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       11.31         6.81        35.90        34.98         6.21        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.76        24.99        16.64        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       23.47        85.55        78.21        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       81.57        73.25        59.51        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       36.79        27.42        33.63        10.65         0.69         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH 
        3.52         8.48        44.88         0.26         4.27        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY 
       39.29        36.62        24.30         9.37        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.36        16.80        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EY-A1G8 
       32.28        34.39        19.36        12.89        27.16        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.90        22.78        13.97        19.27        18.84        17.88 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       12.59         3.62        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CY 
       31.04        13.84         2.14         6.97         5.29        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 
       28.96        25.02        26.01        41.06         1.74         2.43 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.03               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            125.42             191.84 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             16.65              23.70 
[1] "0.0 - 125.4 (16.6)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2"  
D36V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20P GAIN MUTATED                                        43
  20P GAIN WILD-TYPE                                     324
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20P GAIN MUTATED                               4
  20P GAIN WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20P GAIN MUTATED                                  50
  20P GAIN WILD-TYPE                                48
D36V3, multiclass
                                         clus
vv                                        20P GAIN MUTATED 20P GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               43                324
  MIXED SEROUS AND ENDOMETRIOID                          4                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     50                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    16  81
  20P GAIN WILD-TYPE 122 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     16   81
  20P GAIN WILD-TYPE  122  266
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                16                122
  YES               81                266
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED    58   4   7   8
  20P GAIN WILD-TYPE 278  18  10  21
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               58                278
  R1                4                 18
  R2                7                 10
  RX                8                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  1     4
  20P GAIN WILD-TYPE                                3    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P GAIN MUTATED                          21
  20P GAIN WILD-TYPE                        52
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P GAIN MUTATED                                           2    60
  20P GAIN WILD-TYPE                                         7   295
D36V6, multiclass
                                           clus
vv                                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                               21                 52
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   60                295
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2  62
  20P GAIN WILD-TYPE  11 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2   62
  20P GAIN WILD-TYPE   11  274
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               62                274
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    90  22
  20Q GAIN WILD-TYPE 333  38
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               112                371 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                22                 38 
$`20Q GAIN MUTATED`
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       11.44        36.33        46.32        28.64         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3EJ 
        1.18         1.08         0.39         2.40         2.24         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AP-A05A TCGA-AP-A05D 
       22.26         0.92         0.76        16.87        39.42        57.80 
TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A3K1 
      125.42         3.39        97.71        31.30        41.95        18.25 
TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC 
       53.92        28.54        37.78        16.96        20.28        12.43 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FX 
       11.08         4.77        30.12         2.96         0.23         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI 
        0.20        20.52         0.03         0.13         0.23         0.13 
TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11L 
       80.38        43.13        17.85         4.11        75.72        45.90 
TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 
       19.56       191.84       102.31        11.87        12.79         5.03 
TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A0YV 
       34.13        36.49        30.81        24.39        52.83        12.56 
TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A56F TCGA-BS-A0TE 
       15.45         1.81        10.22        24.13        13.18         4.80 
TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A102 TCGA-D1-A169 TCGA-D1-A16I 
       67.20        72.72        49.55         4.44        37.32        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G5 
       29.92        31.07        18.67         0.72         2.07        41.42 
TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 
        4.11        35.38        12.39        91.96        48.36        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AV 
        7.99        10.78        24.79        32.38        19.40        35.15 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GM TCGA-EY-A1GR 
       26.96        22.26        16.34         6.21         6.90        17.62 
TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ 
       15.09         8.55         6.48        14.40        13.45        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2EW 
       27.35         6.44        17.92         3.72        40.01        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-K6-A3WQ 
        9.07        28.93        41.06        13.15 

$`20Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ 
       24.62        29.06        42.35        15.95         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QL 
        8.02        91.04         5.33         5.16         1.97        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK 
        0.85         3.02         0.49         1.12         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49         1.28        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW 
       15.62         1.94        15.95         1.87         1.71         2.33 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89         7.86        12.20        20.91        48.79 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        60.36        55.89        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       33.73         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       15.25        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       25.12        36.39        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G8 TCGA-AX-A3G9 
       31.13        38.70         0.10         0.33         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47        56.91        46.75        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       17.88        13.74        17.10        11.01         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
      113.36        88.34        54.44        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y 
       32.09        33.50        27.35        16.73        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       17.36        16.57        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       15.29        62.14        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        39.32        21.17        20.28        15.42        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       16.34        34.29        28.54        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        14.27         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A6W3 
        6.21        10.16        31.76        24.99        16.64        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG 
        9.86        46.95        23.47        85.55        78.21        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       85.84        82.39        81.57        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16O TCGA-D1-A16Q 
       36.36        37.51        36.79        27.42        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41        13.22        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95         3.52         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
        4.27        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.36        16.80        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EY-A1G8 
       32.28        34.39        19.36        12.89        27.16        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.90        22.78        13.97        19.27        18.84        17.88 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       16.11        12.43        15.81        19.33        12.59         3.62 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 
       18.87        22.82        45.76        31.04        13.84         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        6.97         5.29        34.98        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       13.84         8.98        96.69        28.96        25.02        26.01 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74         2.43        10.82         4.21         5.52 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.03               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            191.84             185.79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             17.29              23.90 
[1] "0.0 - 191.8 (17.3)" "0.1 - 185.8 (23.9)"
[1] "hr=" "2.3"
D37V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20Q GAIN MUTATED                                        49
  20Q GAIN WILD-TYPE                                     318
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20Q GAIN MUTATED                               4
  20Q GAIN WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20Q GAIN MUTATED                                  60
  20Q GAIN WILD-TYPE                                38
D37V3, multiclass
                                         clus
vv                                        20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               49                318
  MIXED SEROUS AND ENDOMETRIOID                          4                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     60                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    20  93
  20Q GAIN WILD-TYPE 118 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     20   93
  20Q GAIN WILD-TYPE  118  254
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                20                118
  YES               93                254
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED    66   5   9   9
  20Q GAIN WILD-TYPE 270  17   8  20
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               66                270
  R1                5                 17
  R2                9                  8
  RX                9                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  1     4
  20Q GAIN WILD-TYPE                                3    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q GAIN MUTATED                          26
  20Q GAIN WILD-TYPE                        47
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q GAIN MUTATED                                           3    70
  20Q GAIN WILD-TYPE                                         6   285
D37V6, multiclass
                                           clus
vv                                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    4                 15
  BLACK OR AFRICAN AMERICAN                               26                 47
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                3                  6
  WHITE                                                   70                285
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     4  72
  20Q GAIN WILD-TYPE   9 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4   72
  20Q GAIN WILD-TYPE    9  264
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  9
  NOT HISPANIC OR LATINO               72                264
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    26   6
  21Q GAIN WILD-TYPE 397  54
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                32                451 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                 54 
$`21Q GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0R6 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BD 
       37.02        19.96         7.33        14.96         1.08         0.49 
TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A1DQ 
       22.26         0.92         1.35         0.76         1.71        41.95 
TCGA-AX-A1C4 TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-B5-A1MY TCGA-B5-A5OD 
       13.28         2.96         0.33        20.52        11.87        34.13 
TCGA-BS-A0U9 TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A22Y 
       67.20        41.42         4.11        91.96        48.36        24.79 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-FI-A2EW 
       27.16        26.96        15.09        13.45        27.35        59.01 
TCGA-FI-A2EX TCGA-FI-A2F9 
        9.07        26.01 

$`21Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       42.35        15.95         7.92        11.44        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.18         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        3.02         1.12         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       14.66        22.49         1.28        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AP-A051 
        1.94        15.95         1.87        16.87         2.33        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       33.73         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       36.39        11.08         4.77        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        27.32        31.13        38.70         0.23         0.10 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.13         0.20         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       12.79        62.14         5.03        41.06        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        35.67        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         1.41         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02         6.77         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH 
        3.52         8.48        44.88         0.26         4.27        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92         7.99        10.78        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH 
       35.05        33.01        27.12        32.28        32.38        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KU TCGA-EO-A3KW 
       34.39        19.36        35.15        12.89        22.26        16.34 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.88        17.62        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       15.81         8.55         6.48        19.33        12.59         3.62 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       14.40        18.87        22.82        45.76        31.04        29.10 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84         6.44        17.92         2.14         6.97         3.72 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.29        40.01        34.98        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       13.84         8.98        96.69        28.93        28.96        25.02 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ 
       41.06         1.74        13.15         2.43        10.82         4.21 
TCGA-QS-A5YR 
        5.52 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.33               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             91.96             191.84 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            17.525             23.210 
[1] "0.3 - 92.0 (17.5)"  "0.0 - 191.8 (23.2)"
[1] "hr=" "2"  
D38V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  21Q GAIN MUTATED                                        11
  21Q GAIN WILD-TYPE                                     356
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  21Q GAIN MUTATED                               1
  21Q GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  21Q GAIN MUTATED                                  20
  21Q GAIN WILD-TYPE                                78
D38V3, multiclass
                                         clus
vv                                        21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               11                356
  MIXED SEROUS AND ENDOMETRIOID                          1                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     20                 78
[1] 3 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, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     6  26
  21Q GAIN WILD-TYPE 132 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      6   26
  21Q GAIN WILD-TYPE  132  321
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 6                132
  YES               26                321
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    22   1   3   2
  21Q GAIN WILD-TYPE 314  21  14  27
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               22                314
  R1                1                 21
  R2                3                 14
  RX                2                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     0
  21Q GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q GAIN MUTATED                           8
  21Q GAIN WILD-TYPE                        65
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q GAIN MUTATED                                           1    19
  21Q GAIN WILD-TYPE                                         8   336
D38V6, multiclass
                                           clus
vv                                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                8                 65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   19                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"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  20
  21Q GAIN WILD-TYPE  13 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   20
  21Q GAIN WILD-TYPE   13  316
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               20                316
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    21   7
  22Q GAIN WILD-TYPE 402  53
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                28                455 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                 53 
$`22Q GAIN MUTATED`
TCGA-A5-A0G5 TCGA-A5-A2K4 TCGA-AP-A05A TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AX-A1CF 
       37.02        28.64        39.42        97.71        18.25        76.83 
TCGA-AX-A2H2 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A1MR TCGA-B5-A3S1 TCGA-BK-A26L 
        4.77         0.13        17.85       191.84         5.03        24.13 
TCGA-D1-A1O0 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EY-A1GO TCGA-EY-A1GS 
        2.07        10.92        10.78        19.40        19.27        15.09 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2CY 
       27.35        13.84         6.44         3.72        40.01        34.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       96.69        59.01         9.07        28.93 

$`22Q GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        91.04        46.32         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        7.33        14.96         1.18         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79         0.85         2.40         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        33.73         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       20.28        12.43        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       25.12        36.39        11.08        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.10         0.33         0.13         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN 
        0.13         0.23         1.18         8.35        14.47        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       15.29        12.79        62.14        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        35.90        34.98         6.21        10.22        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
        4.11        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10        91.96        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
        7.99        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        32.38        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       27.16        26.96        22.26        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.90        22.78        13.97         6.90        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       17.62        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       19.33        12.59         3.62        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A547 TCGA-EY-A548 
       13.45        45.76        31.04        29.10        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
        6.97         5.29        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
        8.98        28.96        25.02        26.01        41.06         1.74 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       13.15         2.43        10.82         4.21         5.52 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.13               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            191.84             185.79 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            19.335             22.920 
[1] "0.1 - 191.8 (19.3)" "0.0 - 185.8 (22.9)"
[1] "hr=" "2.1"
D39V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  22Q GAIN MUTATED                                         7
  22Q GAIN WILD-TYPE                                     360
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  22Q GAIN MUTATED                               1
  22Q GAIN WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  22Q GAIN MUTATED                                  21
  22Q GAIN WILD-TYPE                                77
D39V3, multiclass
                                         clus
vv                                        22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                7                360
  MIXED SEROUS AND ENDOMETRIOID                          1                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     21                 77
[1] 3 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, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     7  22
  22Q GAIN WILD-TYPE 131 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      7   22
  22Q GAIN WILD-TYPE  131  325
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 7                131
  YES               22                325
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED    17   1   4   3
  22Q GAIN WILD-TYPE 319  21  13  26
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               17                319
  R1                1                 21
  R2                4                 13
  RX                3                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     0
  22Q GAIN WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q GAIN MUTATED                          10
  22Q GAIN WILD-TYPE                        63
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q GAIN MUTATED                                           0    15
  22Q GAIN WILD-TYPE                                         9   340
D39V6, multiclass
                                           clus
vv                                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                               10                 63
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   15                340
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  18
  22Q GAIN WILD-TYPE  13 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   18
  22Q GAIN WILD-TYPE   13  318
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               18                318
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    45  13
  XQ GAIN WILD-TYPE 378  47
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               58               425 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               13                47 
$`XQ GAIN MUTATED`
TCGA-A5-A0GV TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3EM TCGA-AJ-A3NG TCGA-AJ-A3TW 
       20.81        14.96         1.08        22.26        15.62         1.71 
TCGA-AP-A0L8 TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05W 
       48.79        33.40        31.30        16.24        33.73        68.35 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-B5-A0JR TCGA-B5-A0JT 
       30.12        33.53        68.71        17.75        56.91        43.13 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A5OD TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       33.50        27.35        34.13        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BK-A0C9 
       34.98         7.92        30.81        15.42        52.83        35.90 
TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT TCGA-BS-A0V8 
       10.22        24.13         4.80        61.87        72.72        49.55 
TCGA-D1-A102 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A17R TCGA-D1-A2G5 TCGA-D1-A2G6 
        4.44         0.66        36.10        11.15        41.42         8.48 
TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EO-A3KU 
       17.06        10.92        24.79        19.40        26.96        22.26 
TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GQ TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 
        6.21        23.34        17.88         6.48        19.33         3.62 
TCGA-EY-A3L3 TCGA-EY-A547 TCGA-FI-A2D4 TCGA-K6-A3WQ 
       27.35        17.92         7.99        13.15 

$`XQ GAIN WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.16         7.33         1.18         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.85         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
        2.24         1.68         1.64        14.66        22.49         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3OJ 
        0.92        36.99        20.65         1.35         0.76         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
       15.95         1.87        16.87         2.33        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
       45.53        36.89         7.86        12.20        20.91       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        18.25         0.56        13.58        19.82        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H8 
       25.12        36.39        11.08         4.77        71.24        61.18 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       33.40        40.50        19.36        26.33        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JU 
        8.35        14.47         0.13        80.38        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       32.09        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 
       11.70        11.87        15.29        12.79        62.14         5.03 
TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M7 TCGA-BG-A0M8 
       41.06        34.95        18.61        20.19        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV 
       43.04        39.32        21.17        20.28        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       16.34        34.29        28.54        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
        6.81        34.98         6.21        10.16        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       85.55        78.21        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        62.79        63.58        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.51         1.78        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DA 
       15.06         1.05         3.95         3.52        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27         4.11        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       35.38         9.37        12.39        31.10        91.96        23.38 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       48.36         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.28        32.38        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       27.16        16.34        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       15.81         8.55        12.59        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR 
       13.45        45.76        31.04        29.10        13.84         6.44 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         3.72         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       33.99        36.00        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
        9.07        28.93        28.96        25.02        26.01        41.06 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74         2.43        10.82         4.21         5.52 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.66              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            72.72            191.84 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            22.26             22.92 
[1] "0.7 - 72.7 (22.3)"  "0.0 - 191.8 (22.9)"
[1] "hr=" "2.2"
D40V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  XQ GAIN MUTATED                                        40
  XQ GAIN WILD-TYPE                                     327
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  XQ GAIN MUTATED                               2
  XQ GAIN WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  XQ GAIN MUTATED                                  16
  XQ GAIN WILD-TYPE                                82
D40V3, multiclass
                                         clus
vv                                        XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              40               327
  MIXED SEROUS AND ENDOMETRIOID                         2                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    16                82
[1] 3 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, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    14  44
  XQ GAIN WILD-TYPE 124 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     14   44
  XQ GAIN WILD-TYPE  124  303
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               14               124
  YES              44               303
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    41   2   5   4
  XQ GAIN WILD-TYPE 295  20  12  25
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              41               295
  R1               2                20
  R2               5                12
  RX               4                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     2
  XQ GAIN WILD-TYPE                                4    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ GAIN MUTATED                           8
  XQ GAIN WILD-TYPE                        65
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ GAIN MUTATED                                           1    42
  XQ GAIN WILD-TYPE                                         8   313
D40V6, multiclass
                                           clus
vv                                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                               8                65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  42               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"
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     1  40
  XQ GAIN WILD-TYPE  12 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1   40
  XQ GAIN WILD-TYPE   12  296
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              40               296
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    17   4
  1P LOSS WILD-TYPE 406  56
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               462 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4                56 
$`1P LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AP-A0L8 
      149.56        60.53        36.33        46.32         1.18        48.79 
TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 
        3.39        97.71        20.28        76.83        11.08         4.77 
TCGA-AX-A2H4 TCGA-B5-A11P TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GO TCGA-EY-A1GP 
       30.12        36.82        27.16        26.96        19.27        18.84 
TCGA-EY-A2OO TCGA-FI-A2EY TCGA-FI-A2F8 
       45.76        28.93        25.02 

$`1P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK 
       42.35        15.95         7.92        11.44         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       91.04        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.08         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        3.02         0.49         1.12         0.76         2.24         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26         1.28         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65         1.35        15.62         0.76         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 
       15.95         1.87        16.87         1.71         2.33        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89         7.86        12.20        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      125.42       117.99       110.37        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       16.96        13.55        15.25        12.43        20.05        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 
       54.12        67.50        25.12        36.39        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.10         0.33         0.13         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 
       11.70        11.87        15.29        12.79        62.14         5.03 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        67.20        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       12.39        31.10        91.96        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       32.28        24.79        32.38        19.40        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       35.15        12.89        22.26        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR 
       23.90        22.78        13.97         6.90        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       19.33        12.59         3.62        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       13.45        31.04        29.10        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       34.98        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV 
       96.69        59.01         9.07        28.96        26.01        41.06 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74        13.15         2.43        10.82         4.21         5.52 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1.18              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           149.56            191.84 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           28.930            22.375 
[1] "1.2 - 149.6 (28.9)" "0.0 - 191.8 (22.4)"
[1] "hr=" "1.3"
D41V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1P LOSS MUTATED                                         6
  1P LOSS WILD-TYPE                                     361
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1P LOSS MUTATED                               3
  1P LOSS WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1P LOSS MUTATED                                  12
  1P LOSS WILD-TYPE                                86
D41V3, multiclass
                                         clus
vv                                        1P LOSS MUTATED 1P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               6               361
  MIXED SEROUS AND ENDOMETRIOID                         3                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    12                86
[1] 3 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, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     6  15
  1P LOSS WILD-TYPE 132 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6   15
  1P LOSS WILD-TYPE  132  332
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                6               132
  YES              15               332
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED    13   2   4   0
  1P LOSS WILD-TYPE 323  20  13  29
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              13               323
  R1               2                20
  R2               4                13
  RX               0                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     1
  1P LOSS WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1P LOSS MUTATED                           5
  1P LOSS WILD-TYPE                        68
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1P LOSS MUTATED                                           0    13
  1P LOSS WILD-TYPE                                         9   342
D41V6, multiclass
                                           clus
vv                                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               5                68
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  13               342
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  14
  1P LOSS WILD-TYPE  13 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   14
  1P LOSS WILD-TYPE   13  322
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                13
  NOT HISPANIC OR LATINO              14               322
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     9   4
  1Q LOSS WILD-TYPE 414  56
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               13               470 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                56 
$`1Q LOSS MUTATED`
TCGA-A5-A0G2 TCGA-AJ-A23M TCGA-AP-A0L8 TCGA-AP-A0LF TCGA-AX-A1CF TCGA-AX-A1CR 
      149.56         1.18        48.79         3.39        76.83        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GP TCGA-FI-A2EY 
        4.77        30.12        27.16        26.96        18.84        28.93 
TCGA-FI-A2F8 
       25.02 

$`1Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33        14.96         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79         0.85         2.40         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        12.20        20.91       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        18.25        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       67.50        25.12        36.39        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.33         0.13         0.20        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         1.18         8.35        14.47         0.13        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       17.88        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 
       11.70        11.87        15.29        12.79        62.14         5.03 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        67.20        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       12.39        31.10        91.96        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       32.28        24.79        32.38        19.40        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       35.15        12.89        22.26        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ 
       23.90        22.78        13.97         6.90        19.27        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        15.09        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59         3.62        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        13.45        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84         6.44        17.92         2.14         6.97         3.72 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.29        40.01        34.98        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 
       13.84         8.98        96.69        59.01         9.07        28.96 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC 
       26.01        41.06         1.74        13.15         2.43        10.82 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.18              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           149.56            191.84 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           26.960            22.665 
[1] "1.2 - 149.6 (27.0)" "0.0 - 191.8 (22.7)"
[1] "hr=" "2.4"
D42V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  1Q LOSS MUTATED                                         3
  1Q LOSS WILD-TYPE                                     364
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  1Q LOSS MUTATED                               2
  1Q LOSS WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  1Q LOSS MUTATED                                   8
  1Q LOSS WILD-TYPE                                90
D42V3, multiclass
                                         clus
vv                                        1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               3               364
  MIXED SEROUS AND ENDOMETRIOID                         2                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     8                90
[1] 3 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, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2  11
  1Q LOSS WILD-TYPE 136 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   11
  1Q LOSS WILD-TYPE  136  336
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                2               136
  YES              11               336
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED     8   1   3   0
  1Q LOSS WILD-TYPE 328  21  14  29
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               8               328
  R1               1                21
  R2               3                14
  RX               0                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     1
  1Q LOSS WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  1Q LOSS MUTATED                           3
  1Q LOSS WILD-TYPE                        70
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  1Q LOSS MUTATED                                           0     7
  1Q LOSS WILD-TYPE                                         9   348
D42V6, multiclass
                                           clus
vv                                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               3                70
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                   7               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"
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     0   9
  1Q LOSS WILD-TYPE  13 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      0    9
  1Q LOSS WILD-TYPE   13  327
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                13
  NOT HISPANIC OR LATINO               9               327
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     7   3
  2P LOSS WILD-TYPE 416  57
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               10               473 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                57 
$`2P LOSS MUTATED`
TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AW-A1PO TCGA-AX-A2H4 TCGA-BG-A18C TCGA-BS-A0U9 
        0.49        22.26         0.56        30.12        15.45        67.20 
TCGA-D1-A1O0 TCGA-EY-A1GW TCGA-FI-A2F9 TCGA-FI-A3PV 
        2.07         8.55        26.01        41.06 

$`2P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76         2.24         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S 
       10.42        27.85        16.24        18.25        33.73        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
        4.77        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       15.29        12.79        62.14         5.03        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98         7.92        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       12.56        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        35.90        34.98         6.21        10.22        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.76        24.99        24.13        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
        4.11        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10        91.96        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       27.12        32.28        24.79        32.38        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.36        35.15        12.89        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
        6.90        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        15.81         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
        3.62        14.40        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       31.04        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         3.72         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-H5-A2HR 
       59.01         9.07        28.93        28.96        25.02         1.74 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       13.15         2.43        10.82         4.21         5.52 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.49              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            67.20            191.84 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           18.855            22.920 
[1] "0.5 - 67.2 (18.9)"  "0.0 - 191.8 (22.9)"
[1] "hr=" "3.3"
D43V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2P LOSS MUTATED                                         7
  2P LOSS WILD-TYPE                                     360
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2P LOSS MUTATED                               0
  2P LOSS WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2P LOSS MUTATED                                   3
  2P LOSS WILD-TYPE                                95
D43V3, multiclass
                                         clus
vv                                        2P LOSS MUTATED 2P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               7               360
  MIXED SEROUS AND ENDOMETRIOID                         0                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     3                95
[1] 3 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, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0  10
  2P LOSS WILD-TYPE 138 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   10
  2P LOSS WILD-TYPE  138  337
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                0               138
  YES              10               337
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     6   1   1   2
  2P LOSS WILD-TYPE 330  21  16  27
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               6               330
  R1               1                21
  R2               1                16
  RX               2                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     0
  2P LOSS WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2P LOSS MUTATED                           1
  2P LOSS WILD-TYPE                        72
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2P LOSS MUTATED                                           1     8
  2P LOSS WILD-TYPE                                         8   347
D43V6, multiclass
                                           clus
vv                                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                               1                72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                   8               347
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1   8
  2P LOSS WILD-TYPE  12 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1    8
  2P LOSS WILD-TYPE   12  328
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO               8               328
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    11   5
  2Q LOSS WILD-TYPE 412  55
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               16               467 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                55 
$`2Q LOSS MUTATED`
TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3QS TCGA-AP-A0L8 TCGA-AW-A1PO TCGA-AX-A2H4 
        0.49        22.26        16.87        48.79         0.56        30.12 
TCGA-AX-A3G1 TCGA-BG-A18C TCGA-BS-A0U9 TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-EY-A1GC 
       20.52        15.45        67.20         2.07         4.27         4.54 
TCGA-EY-A1GW TCGA-EY-A2OQ TCGA-FI-A2F9 TCGA-FI-A3PV 
        8.55        29.10        26.01        41.06 

$`2Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76         2.24         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW 
       15.62         0.76         1.94        15.95         1.87         1.71 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.33        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       12.20        20.91       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        18.25        33.73        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 
       67.50        25.12        36.39        11.08         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 
        0.23         0.10         0.33         0.13         0.20         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC 
       14.70        11.70        11.87        15.29        12.79        62.14 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
        5.03        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       44.88         0.26         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92         7.99        10.78        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       35.05        33.01        27.12        32.28        24.79        32.38 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        19.36        35.15        12.89        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       26.96        22.26        16.34         6.21        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       13.97         6.90        19.27        18.84        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       15.09        16.11        12.43        15.81         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59         3.62        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       45.76        31.04        27.35        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         3.72         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-H5-A2HR 
       59.01         9.07        28.93        28.96        25.02         1.74 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       13.15         2.43        10.82         4.21         5.52 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.49              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            67.20            191.84 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           18.695            23.010 
[1] "0.5 - 67.2 (18.7)"  "0.0 - 191.8 (23.0)"
[1] "hr=" "3.5"
D44V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  2Q LOSS MUTATED                                        11
  2Q LOSS WILD-TYPE                                     356
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  2Q LOSS MUTATED                               0
  2Q LOSS WILD-TYPE                            20
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  2Q LOSS MUTATED                                   5
  2Q LOSS WILD-TYPE                                93
D44V3, multiclass
                                         clus
vv                                        2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              11               356
  MIXED SEROUS AND ENDOMETRIOID                         0                20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     5                93
[1] 3 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, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1  15
  2Q LOSS WILD-TYPE 137 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   15
  2Q LOSS WILD-TYPE  137  332
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                1               137
  YES              15               332
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    11   1   1   2
  2Q LOSS WILD-TYPE 325  21  16  27
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              11               325
  R1               1                21
  R2               1                16
  RX               2                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     0
  2Q LOSS WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  2Q LOSS MUTATED                           3
  2Q LOSS WILD-TYPE                        70
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  2Q LOSS MUTATED                                           1    12
  2Q LOSS WILD-TYPE                                         8   343
D44V6, multiclass
                                           clus
vv                                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                               3                70
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  12               343
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1  13
  2Q LOSS WILD-TYPE  12 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   13
  2Q LOSS WILD-TYPE   12  323
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              13               323
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    38   8
  3P LOSS WILD-TYPE 385  52
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               46               437 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8                52 
$`3P LOSS MUTATED`
TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3TW 
       11.44        46.32         1.18         1.12         1.64         1.71 
TCGA-AP-A052 TCGA-AP-A05D TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
       21.99        57.80       125.42        97.71        41.95        18.25 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HK 
        0.56        37.78        36.39        11.08        61.18         2.96 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0KB TCGA-B5-A11I 
        0.13         0.13        80.38        23.01         4.11        75.72 
TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-D1-A0ZZ 
        7.92        12.56        15.45        16.64        61.87        22.55 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-DI-A1NN TCGA-EO-A3KW 
       31.07        18.67         0.72         2.07        35.38        16.34 
TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GV TCGA-EY-A2OQ TCGA-EY-A3L3 
       23.90        19.27        18.84        15.81        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EY 
       13.84         3.72        36.00        28.93 

$`3P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH 
       24.62        29.06        42.35        15.95         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        91.04        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33        14.96         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI 
        0.85         2.40         3.02         0.49         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.68        14.66        22.49        22.26         1.28         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65         1.35        15.62         0.76         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A053 
       15.95         1.87        16.87         2.33        83.67         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07         8.22        39.42        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        12.20        20.91        48.79       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       33.73        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        72.56        54.12        67.50        25.12         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        71.24        33.53        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.10         0.33         0.13         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.03         0.23         1.18         8.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       88.34        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       62.14         5.03        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        34.98        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
       10.22        10.16        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        4.80        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O 
       37.51        36.79        27.42        11.51        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27         4.11        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30         9.37        12.39        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92         7.99        10.78        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       35.05        33.01        27.12        32.28        24.79        32.38 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        19.36        35.15        12.89        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       26.96        22.26         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
        6.90        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
        8.55         6.48        19.33        12.59         3.62        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR 
       18.87        22.82        13.45        45.76        31.04         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
       17.92         2.14         6.97         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       33.99         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
        9.07        28.96        25.02        26.01        41.06         1.74 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       13.15         2.43        10.82         4.21         5.52 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.13              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           125.42            191.84 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           18.755            23.340 
[1] "0.1 - 125.4 (18.8)" "0.0 - 191.8 (23.3)"
[1] "hr=" "1.6"
D45V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3P LOSS MUTATED                                        16
  3P LOSS WILD-TYPE                                     351
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3P LOSS MUTATED                               6
  3P LOSS WILD-TYPE                            14
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3P LOSS MUTATED                                  24
  3P LOSS WILD-TYPE                                74
D45V3, multiclass
                                         clus
vv                                        3P LOSS MUTATED 3P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              16               351
  MIXED SEROUS AND ENDOMETRIOID                         6                14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    24                74
[1] 3 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, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    11  35
  3P LOSS WILD-TYPE 127 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     11   35
  3P LOSS WILD-TYPE  127  312
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               11               127
  YES              35               312
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED    33   2   2   2
  3P LOSS WILD-TYPE 303  20  15  27
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              33               303
  R1               2                20
  R2               2                15
  RX               2                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     1
  3P LOSS WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3P LOSS MUTATED                          12
  3P LOSS WILD-TYPE                        61
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3P LOSS MUTATED                                           1    31
  3P LOSS WILD-TYPE                                         8   324
D45V6, multiclass
                                           clus
vv                                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                              12                61
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  31               324
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0  34
  3P LOSS WILD-TYPE  13 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0   34
  3P LOSS WILD-TYPE   13  302
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                13
  NOT HISPANIC OR LATINO              34               302
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    25   4
  3Q LOSS WILD-TYPE 398  56
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               29               454 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4                56 
$`3Q LOSS MUTATED`
TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A3BF TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A05D 
       46.32         1.18         1.12         1.71        21.99        57.80 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A0IW TCGA-AX-A2H8 
      125.42        97.71        41.95        18.25        37.78        61.18 
TCGA-AX-A2HK TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB 
        2.96         0.13         0.13        80.38        17.85         4.11 
TCGA-BK-A4ZD TCGA-D1-A16S TCGA-D1-A1O0 TCGA-EO-A3AZ TCGA-EY-A1GJ TCGA-EY-A1GO 
       16.64        18.67         2.07        27.16        23.90        19.27 
TCGA-EY-A1GP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2D2 
       18.84        29.10        27.35         3.72        36.00 

$`3Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33         9.60         8.02        91.04        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33        14.96         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG 
       19.79         0.85         2.40         3.02         0.49         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        2.24         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
        1.28         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW 
        0.76         1.94        15.95         1.87        16.87         2.33 
TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       83.67         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89         7.86        12.20        20.91        48.79 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       31.30        35.54        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       71.24        33.53        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        27.32        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.10         0.33         0.13         0.20        20.52         0.03 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.23         1.18         8.35        14.47        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        11.01         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       62.14         5.03        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        35.67        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        24.13        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH 
        8.48        44.88         0.26         4.27         4.11        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10        91.96        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        6.67        16.01         7.36        16.80        10.92         7.99 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.78        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       24.79        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        26.96        22.26        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       22.78        13.97         6.90        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59         3.62        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       45.76        31.04        13.84         6.44        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        6.97         5.29        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ 
       28.96        25.02        26.01        41.06         1.74        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        2.43        10.82         4.21         5.52 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.13              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           125.42            191.84 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           19.270            22.965 
[1] "0.1 - 125.4 (19.3)" "0.0 - 191.8 (23.0)"
[1] "hr=" "1.2"
D46V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  3Q LOSS MUTATED                                        10
  3Q LOSS WILD-TYPE                                     357
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  3Q LOSS MUTATED                               2
  3Q LOSS WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  3Q LOSS MUTATED                                  17
  3Q LOSS WILD-TYPE                                81
D46V3, multiclass
                                         clus
vv                                        3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              10               357
  MIXED SEROUS AND ENDOMETRIOID                         2                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    17                81
[1] 3 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, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5  24
  3Q LOSS WILD-TYPE 133 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   24
  3Q LOSS WILD-TYPE  133  323
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                5               133
  YES              24               323
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    20   0   2   1
  3Q LOSS WILD-TYPE 316  22  15  28
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              20               316
  R1               0                22
  R2               2                15
  RX               1                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     0
  3Q LOSS WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  3Q LOSS MUTATED                          10
  3Q LOSS WILD-TYPE                        63
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  3Q LOSS MUTATED                                           1    17
  3Q LOSS WILD-TYPE                                         8   338
D46V6, multiclass
                                           clus
vv                                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                              10                63
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  17               338
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  18
  3Q LOSS WILD-TYPE  13 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   18
  3Q LOSS WILD-TYPE   13  318
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                13
  NOT HISPANIC OR LATINO              18               318
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    70  16
  4P LOSS WILD-TYPE 353  44
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               86               397 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               16                44 
$`4P LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-A5-A2K2 
      149.56        60.53        36.82        19.96        36.33        91.04 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A2QM 
       28.64         7.33        14.96         1.18         0.39         0.85 
TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW 
        0.49         1.64         1.35         0.76        16.87         1.71 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LO 
        5.95        57.80        45.53       125.42         3.39        33.40 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CC 
       18.25         0.56        53.92        37.78        20.28        12.43 
TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF 
       76.83        11.08         4.77        30.12        61.18        19.36 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        2.96        38.70         0.23        20.52         0.03         0.13 
TCGA-B5-A0JX TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A3S1 
       44.71        17.85        75.72        36.82        11.87         5.03 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC 
       34.13        34.95        36.49        12.56         6.81        10.22 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16R 
       24.13        67.20        49.55        39.48        37.32         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-DI-A1NN 
       18.67         1.41         6.77         0.72         2.07        35.38 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GO 
       12.39        91.96        27.16        22.26         4.54        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO 
       18.84        17.62         3.62        14.40        13.45        45.76 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       27.35        13.84         9.07        28.93        25.02        41.06 
TCGA-K6-A3WQ TCGA-PG-A5BC 
       13.15        10.82 

$`4P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 
        7.92        11.44         9.60         8.02        46.32         5.33 
TCGA-A5-A2K7 TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
        5.16         1.08         1.97        19.79         2.40         3.02 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76         2.24         1.68        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.26         1.28         0.92        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
        1.94        15.95         1.87         2.33        83.67        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07         8.22        39.42        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.20        20.91        48.79       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
        6.71        30.90        10.42        27.85        16.24        33.73 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       15.25        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       36.39        71.24        33.53        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FW 
       26.33        17.75        27.32        31.13         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.13         0.20         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.13        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB 
       23.01        17.88        13.74        17.10        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       12.79        62.14        41.06        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.94        35.21        34.98         7.92        38.37        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       11.31        35.90        34.98         6.21        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       31.07        33.63        10.65         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41        13.22        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       24.30         9.37        31.10        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       32.28        24.79        32.38        19.40        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       35.15        12.89        26.96        16.34         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT 
       22.78        13.97         6.90        17.88        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81         8.55         6.48        19.33        12.59 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 
       18.87        22.82        31.04        29.10         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         3.72         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-QS-A5YQ 
       59.01        28.96        26.01         1.74         2.43         4.21 
TCGA-QS-A5YR 
        5.52 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.03              0.10 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           149.56            191.84 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            18.46             23.47 
[1] "0.0 - 149.6 (18.5)" "0.1 - 191.8 (23.5)"
[1] "hr=" "1.9"
D47V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4P LOSS MUTATED                                        29
  4P LOSS WILD-TYPE                                     338
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4P LOSS MUTATED                               5
  4P LOSS WILD-TYPE                            15
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4P LOSS MUTATED                                  52
  4P LOSS WILD-TYPE                                46
D47V3, multiclass
                                         clus
vv                                        4P LOSS MUTATED 4P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              29               338
  MIXED SEROUS AND ENDOMETRIOID                         5                15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    52                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    18  68
  4P LOSS WILD-TYPE 120 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     18   68
  4P LOSS WILD-TYPE  120  279
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               18               120
  YES              68               279
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED    55   5   5   5
  4P LOSS WILD-TYPE 281  17  12  24
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              55               281
  R1               5                17
  R2               5                12
  RX               5                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  1     1
  4P LOSS WILD-TYPE                                3    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4P LOSS MUTATED                          15
  4P LOSS WILD-TYPE                        58
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4P LOSS MUTATED                                           3    63
  4P LOSS WILD-TYPE                                         6   292
D47V6, multiclass
                                           clus
vv                                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                              15                58
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                  63               292
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     4  61
  4P LOSS WILD-TYPE   9 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      4   61
  4P LOSS WILD-TYPE    9  275
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 9
  NOT HISPANIC OR LATINO              61               275
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    69  17
  4Q LOSS WILD-TYPE 354  43
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               86               397 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               17                43 
$`4Q LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG 
      149.56        65.75        60.53        36.82        19.96        11.44 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       36.33        91.04        28.64         7.33         1.18         1.08 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS 
        0.85         0.49         1.64         1.35         0.76        16.87 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO 
       57.80        45.53       125.42         3.39        97.71        33.40 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF 
       18.25         0.56        37.78        20.28        12.43        76.83 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK 
       11.08         4.77        30.12        61.18        19.36         2.96 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-B5-A0JN TCGA-B5-A11I 
       38.70         0.23        20.52         0.13        80.38        75.72 
TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD 
       36.82        50.89        11.87        12.79         5.03        34.13 
TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A26L TCGA-BS-A0U9 
       34.95        36.49        12.56         6.81        24.13        67.20 
TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       49.55        39.48        37.32         0.69        18.67         1.41 
TCGA-D1-A179 TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NN 
        6.77         0.72         2.07         4.27         4.11        35.38 
TCGA-DI-A1NO TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO 
        9.37        27.16        22.26         4.54         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A3L3 
       18.84        17.62         3.62        14.40        45.76        27.35 
TCGA-EY-A3QX TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-K6-A3WQ 
       13.84         9.07        28.93        25.02        41.06        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC 
        2.43        10.82 

$`4Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP 
      105.37        87.32        74.10        57.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 
       38.37        28.27        20.81        23.21        68.65        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
        9.60         8.02        46.32         5.33         5.16        14.96 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        1.97         0.39        19.79         2.40         3.02         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        0.76         2.24         1.68        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
        1.28         0.92        36.99        20.65        15.62         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
       15.95         1.87         1.71         2.33        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J 
        5.95        23.31        86.07         8.22        39.42        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        12.20        20.91        48.79       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
        6.71        30.90        10.42        27.85        16.24        33.73 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       13.55        15.25        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       25.12        36.39        71.24        33.53        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FT 
       40.50        26.33        17.75        27.32        31.13         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.33         0.13         0.20         0.03         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        8.35        14.47         0.13        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        54.44        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       191.84       102.31        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       11.70        15.29        62.14        41.06        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       20.12        11.31        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.16        31.76        24.99        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16X 
       11.51        29.92        31.07        33.63        10.65         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41        13.22        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        8.48        44.88         0.26        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
       24.30        12.39        31.10        91.96        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       27.12        32.28        24.79        32.38        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 
       19.36        35.15        12.89        26.96        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT 
       23.90        22.78        13.97        17.88        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81         8.55         6.48        19.33        12.59 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR 
       18.87        22.82        13.45        31.04        29.10         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       34.98        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-QS-A5YQ 
       96.69        59.01        28.96        26.01         1.74         4.21 
TCGA-QS-A5YR 
        5.52 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.13              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           149.56            191.84 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           18.755            23.380 
[1] "0.1 - 149.6 (18.8)" "0.0 - 191.8 (23.4)"
[1] "hr=" "2.1"
D48V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  4Q LOSS MUTATED                                        29
  4Q LOSS WILD-TYPE                                     338
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  4Q LOSS MUTATED                               6
  4Q LOSS WILD-TYPE                            14
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  4Q LOSS MUTATED                                  51
  4Q LOSS WILD-TYPE                                47
D48V3, multiclass
                                         clus
vv                                        4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              29               338
  MIXED SEROUS AND ENDOMETRIOID                         6                14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    51                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    18  68
  4Q LOSS WILD-TYPE 120 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     18   68
  4Q LOSS WILD-TYPE  120  279
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               18               120
  YES              68               279
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED    56   5   5   4
  4Q LOSS WILD-TYPE 280  17  12  25
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              56               280
  R1               5                17
  R2               5                12
  RX               4                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     2
  4Q LOSS WILD-TYPE                                4    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  4Q LOSS MUTATED                          18
  4Q LOSS WILD-TYPE                        55
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  4Q LOSS MUTATED                                           3    60
  4Q LOSS WILD-TYPE                                         6   295
D48V6, multiclass
                                           clus
vv                                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                              18                55
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               3                 6
  WHITE                                                  60               295
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     2  60
  4Q LOSS WILD-TYPE  11 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2   60
  4Q LOSS WILD-TYPE   11  276
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO              60               276
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    37  11
  5P LOSS WILD-TYPE 386  49
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               48               435 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11                49 
$`5P LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A2QM 
      149.56        19.96        17.59         7.33         1.18         0.85 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3QS TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF 
        1.64        22.26        16.87        48.79       125.42         3.39 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A2H4 TCGA-AX-A2HF 
       97.71        33.40        18.25        53.92        30.12        19.36 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1N2 
        0.13         0.20        17.85         4.11        75.72        12.79 
TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L 
        5.03        34.95        36.49         6.81        10.22        24.13 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A16V 
       16.64        67.20        39.48        11.51        18.67         1.41 
TCGA-D1-A179 TCGA-D1-A1NU TCGA-DI-A2QY TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EY-A1GO 
        6.77        13.22        91.96        32.38        22.26        19.27 
TCGA-EY-A1GP TCGA-EY-A212 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A3PV TCGA-KJ-A3U4 
       18.84         3.62        13.84         6.44        41.06         2.43 

$`5P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       23.21        68.65        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
       91.04        46.32        28.64         5.33         5.16        14.96 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.08         1.97         0.39        19.79         2.40         3.02 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
        0.49         1.12         0.76         2.24         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW 
       15.62         0.76         1.94        15.95         1.87         1.71 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.33        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       12.20        20.91       117.99       110.37        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        33.73         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.23         0.10         0.33        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         1.18         8.35        14.47         0.13        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       17.88        13.74        17.10        11.01         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.94        35.21        34.98         7.92        38.37        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31        35.90        34.98         6.21        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.76        24.99        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X 
       29.92        31.07        33.63        10.65         0.69         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       12.39        31.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        6.67        16.01         7.36        16.80        10.92         7.99 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.78        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       27.16        26.96        16.34         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       22.78        13.97         6.90        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       12.59        14.40        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       31.04        29.10        27.35        17.92         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
        3.72         5.29        40.01        34.98        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ 
       28.93        28.96        25.02        26.01         1.74        13.15 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.13              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           149.56            191.84 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            18.05             23.47 
[1] "0.1 - 149.6 (18.1)" "0.0 - 191.8 (23.5)"
[1] "hr=" "2.3"
D49V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5P LOSS MUTATED                                        16
  5P LOSS WILD-TYPE                                     351
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5P LOSS MUTATED                               1
  5P LOSS WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5P LOSS MUTATED                                  31
  5P LOSS WILD-TYPE                                67
D49V3, multiclass
                                         clus
vv                                        5P LOSS MUTATED 5P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              16               351
  MIXED SEROUS AND ENDOMETRIOID                         1                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    31                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    17  31
  5P LOSS WILD-TYPE 121 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     17   31
  5P LOSS WILD-TYPE  121  316
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               17               121
  YES              31               316
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    29   0   3   6
  5P LOSS WILD-TYPE 307  22  14  23
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              29               307
  R1               0                22
  R2               3                14
  RX               6                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     2
  5P LOSS WILD-TYPE                                4    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5P LOSS MUTATED                          12
  5P LOSS WILD-TYPE                        61
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5P LOSS MUTATED                                           1    31
  5P LOSS WILD-TYPE                                         8   324
D49V6, multiclass
                                           clus
vv                                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                              12                61
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  31               324
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  32
  5P LOSS WILD-TYPE  10 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   32
  5P LOSS WILD-TYPE   10  304
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                10
  NOT HISPANIC OR LATINO              32               304
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    51  14
  5Q LOSS WILD-TYPE 372  46
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               65               418 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               14                46 
$`5Q LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OH TCGA-A5-A3LO TCGA-AJ-A23M 
      149.56        19.96        17.59        36.33         7.33         1.18 
TCGA-AJ-A2QM TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS 
        0.85         1.64        22.26         0.92         0.76        16.87 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AX-A06B 
       45.53        48.79       125.42        97.71        33.40        53.92 
TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HF 
       37.78        20.28        76.83         4.77        30.12        19.36 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MU 
        0.13         0.20        17.85         4.11        75.72        50.89 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 
       12.79         5.03        34.13        34.95         7.92        36.49 
TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
       12.56         6.81        10.22        10.16        24.13        16.64 
TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A179 
       67.20        22.55        39.48        11.51        18.67         6.77 
TCGA-D1-A1NU TCGA-DI-A1NO TCGA-DI-A2QY TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3KU 
       13.22         9.37        91.96        32.38        27.16        22.26 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A3QX 
       19.27        18.84         8.55         3.62        14.40        13.84 
TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-KJ-A3U4 
        6.44        36.00        25.02        41.06         2.43 

$`5Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       23.21        68.65        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       15.95         7.92        11.44         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23N 
       46.32        28.64         5.33         5.16        14.96         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        1.97         0.39        19.79         2.40         3.02         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76         2.24         1.68        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
        1.28        36.99        20.65         1.35        15.62         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
       15.95         1.87         1.71         2.33        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        39.42        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89         7.86        12.20        20.91       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       18.25        33.73         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       34.98        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        28.54        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       19.20        16.96        13.55        15.25        12.43        20.05 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.23         0.10         0.33        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         1.18         8.35        14.47         0.13        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       17.88        13.74        17.10        11.01         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FC 
       14.40        14.70        11.70        11.87        15.29        62.14 
TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       41.06        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       34.98        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       28.54        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
        6.21        31.76        24.99        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74         4.44        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       29.92        31.07        33.63        10.65         0.69         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
        4.11        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       12.39        31.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        6.67        16.01         7.36        16.80        10.92         7.99 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.78        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       26.96        16.34         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       13.97         6.90        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 
       12.43        15.81         6.48        19.33        12.59        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        13.45        45.76        31.04        29.10        27.35 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       34.98        33.99         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR 
       59.01         9.07        28.93        28.96        26.01         1.74 
TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       13.15        10.82         4.21         5.52 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.13              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           149.56            191.84 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           18.840            23.425 
[1] "0.1 - 149.6 (18.8)" "0.0 - 191.8 (23.4)"
[1] "hr=" "2.1"
D50V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  5Q LOSS MUTATED                                        19
  5Q LOSS WILD-TYPE                                     348
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  5Q LOSS MUTATED                               4
  5Q LOSS WILD-TYPE                            16
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  5Q LOSS MUTATED                                  43
  5Q LOSS WILD-TYPE                                55
D50V3, multiclass
                                         clus
vv                                        5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              19               348
  MIXED SEROUS AND ENDOMETRIOID                         4                16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    43                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    21  45
  5Q LOSS WILD-TYPE 117 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     21   45
  5Q LOSS WILD-TYPE  117  302
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               21               117
  YES              45               302
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED    42   2   3   6
  5Q LOSS WILD-TYPE 294  20  14  23
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              42               294
  R1               2                20
  R2               3                14
  RX               6                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     2
  5Q LOSS WILD-TYPE                                4    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  5Q LOSS MUTATED                          16
  5Q LOSS WILD-TYPE                        57
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  5Q LOSS MUTATED                                           1    44
  5Q LOSS WILD-TYPE                                         8   311
D50V6, multiclass
                                           clus
vv                                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                              16                57
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  44               311
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     4  43
  5Q LOSS WILD-TYPE   9 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4   43
  5Q LOSS WILD-TYPE    9  293
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 9
  NOT HISPANIC OR LATINO              43               293
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    13   2
  6P LOSS WILD-TYPE 410  58
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               15               468 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                58 
$`6P LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A05J 
      149.56        60.53        19.96         0.76        57.80        36.89 
TCGA-AP-A0L9 TCGA-AX-A1C7 TCGA-AX-A2H4 TCGA-B5-A11P TCGA-BG-A3PP TCGA-EY-A2OQ 
      125.42        16.96        30.12        36.82         6.81        29.10 
TCGA-FI-A2D2 TCGA-FI-A3PV TCGA-KJ-A3U4 
       36.00        41.06         2.43 

$`6P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.85         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        2.24         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
        1.28         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       39.42        45.53         7.86        12.20        20.91        48.79 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       19.20        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       11.08         4.77        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.13         0.20        20.52         0.03         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18         8.35        14.47         0.13        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       15.29        12.79        62.14         5.03        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98         7.92        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       11.31        35.90        34.98         6.21        10.22        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.76        24.99        24.13        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92         7.99        10.78        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       35.05        33.01        27.12        32.28        24.79        32.38 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        19.36        35.15        12.89        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       26.96        22.26        16.34         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        15.09        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59         3.62        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        13.45        45.76        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
        6.44        17.92         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        34.98        33.99         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       96.69        59.01         9.07        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       26.01         1.74        13.15        10.82         4.21         5.52 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.76              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           149.56            191.84 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            36.00             22.52 
[1] "0.8 - 149.6 (36.0)" "0.0 - 191.8 (22.5)"
[1] "hr=" "1.4"
D51V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6P LOSS MUTATED                                         3
  6P LOSS WILD-TYPE                                     364
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6P LOSS MUTATED                               1
  6P LOSS WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6P LOSS MUTATED                                  11
  6P LOSS WILD-TYPE                                87
D51V3, multiclass
                                         clus
vv                                        6P LOSS MUTATED 6P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               3               364
  MIXED SEROUS AND ENDOMETRIOID                         1                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    11                87
[1] 3 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, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  10
  6P LOSS WILD-TYPE 133 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   10
  6P LOSS WILD-TYPE  133  337
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                5               133
  YES              10               337
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    13   0   1   0
  6P LOSS WILD-TYPE 323  22  16  29
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              13               323
  R1               0                22
  R2               1                16
  RX               0                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     1
  6P LOSS WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6P LOSS MUTATED                           1
  6P LOSS WILD-TYPE                        72
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6P LOSS MUTATED                                           0    12
  6P LOSS WILD-TYPE                                         9   343
D51V6, multiclass
                                           clus
vv                                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               1                72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  12               343
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1   9
  6P LOSS WILD-TYPE  12 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1    9
  6P LOSS WILD-TYPE   12  327
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO               9               327
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    18   4
  6Q LOSS WILD-TYPE 405  56
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22               461 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                4                56 
$`6Q LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A3BF TCGA-AJ-A3IA TCGA-AJ-A3NH 
      149.56        60.53        19.96         1.12         0.92         0.76 
TCGA-AJ-A3QS TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AW-A1PO TCGA-AX-A1C7 
       16.87        57.80        36.89       125.42         0.56        16.96 
TCGA-AX-A2H4 TCGA-B5-A11P TCGA-B5-A1MY TCGA-BG-A3PP TCGA-D1-A16I TCGA-EO-A3B1 
       30.12        36.82        11.87         6.81        11.51        26.96 
TCGA-EY-A2OQ TCGA-FI-A2D2 TCGA-FI-A3PV TCGA-KJ-A3U4 
       29.10        36.00        41.06         2.43 

$`6Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI 
        0.85         2.40         3.02         0.49         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26         1.28 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65         1.35        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
        1.87         1.71         2.33        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N 
       23.31        86.07         8.22        39.42        45.53         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       12.20        20.91        48.79       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        18.25        33.73        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       65.88        13.28        19.20        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 
       25.12        36.39        11.08         4.77        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.10         0.33         0.13         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       11.70        15.29        12.79        62.14         5.03        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       20.12        11.31        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       10.16        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92         7.99        10.78        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       35.05        33.01        27.12        32.28        24.79        32.38 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        19.36        35.15        12.89        27.16 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       22.26        16.34         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       13.97         6.90        19.27        18.84        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       19.33        12.59         3.62        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       13.45        45.76        31.04        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       34.98        33.99         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        26.01 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74        13.15        10.82         4.21         5.52 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.56              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           149.56            191.84 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            23.46             22.82 
[1] "0.6 - 149.6 (23.5)" "0.0 - 191.8 (22.8)"
[1] "hr=" "1.4"
D52V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  6Q LOSS MUTATED                                         4
  6Q LOSS WILD-TYPE                                     363
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  6Q LOSS MUTATED                               1
  6Q LOSS WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  6Q LOSS MUTATED                                  17
  6Q LOSS WILD-TYPE                                81
D52V3, multiclass
                                         clus
vv                                        6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               4               363
  MIXED SEROUS AND ENDOMETRIOID                         1                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    17                81
[1] 3 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, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     7  15
  6Q LOSS WILD-TYPE 131 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7   15
  6Q LOSS WILD-TYPE  131  332
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                7               131
  YES              15               332
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    19   0   1   0
  6Q LOSS WILD-TYPE 317  22  16  29
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              19               317
  R1               0                22
  R2               1                16
  RX               0                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     1
  6Q LOSS WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  6Q LOSS MUTATED                           3
  6Q LOSS WILD-TYPE                        70
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  6Q LOSS MUTATED                                           0    16
  6Q LOSS WILD-TYPE                                         9   339
D52V6, multiclass
                                           clus
vv                                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                               3                70
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  16               339
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1  14
  6Q LOSS WILD-TYPE  12 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   14
  6Q LOSS WILD-TYPE   12  322
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              14               322
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    30   9
  7P LOSS WILD-TYPE 393  51
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               39               444 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                9                51 
$`7P LOSS MUTATED`
TCGA-A5-A0R6 TCGA-AJ-A23M TCGA-AP-A054 TCGA-AP-A0L8 TCGA-AP-A1DQ TCGA-AX-A06B 
       19.96         1.18        23.31        48.79        41.95        53.92 
TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IO 
       20.28        11.08         4.77        27.32         2.96        38.70 
TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-BG-A3PP TCGA-BK-A0CC 
       80.38        17.85         4.11        75.72         6.81        10.22 
TCGA-BS-A0U9 TCGA-D1-A16V TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN 
       67.20         1.41         2.07        44.88         4.11        35.38 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EC-A1NJ TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EO-A3KU 
       91.96        48.36        16.01        10.78        19.40        22.26 
TCGA-EY-A1GC TCGA-EY-A212 TCGA-EY-A2OO TCGA-EY-A547 TCGA-FI-A2EW TCGA-FI-A2F8 
        4.54         3.62        45.76        17.92        59.01        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-PG-A5BC 
       26.01        41.06        10.82 

$`7P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        23.21        68.65        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33        14.96         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79         0.85         2.40         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A056 
        1.71         2.33        83.67        21.99         5.95        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       12.20        20.91       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       18.25        33.73         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       34.98        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC 
       13.28        19.20        16.96        13.55        15.25        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       36.39        30.12        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2IN 
       33.40        40.50        19.36        26.33        17.75        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.10         0.33         0.13         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.03         0.13         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.13        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       23.01        17.88        13.74        17.10        11.01         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       15.29        12.79        62.14         5.03        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98         7.92        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       11.31        35.90        34.98         6.21        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        8.48         0.26         4.27        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       24.30         9.37        12.39        31.10        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        2.37         6.67         7.36        16.80        10.92         7.99 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        32.28        24.79 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       32.38        34.39        19.36        35.15        12.89        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       26.96        16.34         6.21        14.99         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
        6.90        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP 
       12.59        14.40        18.87        22.82        13.45        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 
       29.10        27.35        13.84         6.44         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
        3.72         5.29        40.01        34.98        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        13.84         8.98        96.69         9.07        28.93 
TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-QS-A5YQ TCGA-QS-A5YR 
       28.96         1.74        13.15         2.43         4.21         5.52 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1.18              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            91.96            191.84 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           20.280            22.965 
[1] "1.2 - 92.0 (20.3)"  "0.0 - 191.8 (23.0)"
[1] "hr=" "2.1"
D53V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7P LOSS MUTATED                                        14
  7P LOSS WILD-TYPE                                     353
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7P LOSS MUTATED                               2
  7P LOSS WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7P LOSS MUTATED                                  23
  7P LOSS WILD-TYPE                                75
D53V3, multiclass
                                         clus
vv                                        7P LOSS MUTATED 7P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              14               353
  MIXED SEROUS AND ENDOMETRIOID                         2                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    23                75
[1] 3 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, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     8  31
  7P LOSS WILD-TYPE 130 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      8   31
  7P LOSS WILD-TYPE  130  316
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                8               130
  YES              31               316
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    25   4   1   3
  7P LOSS WILD-TYPE 311  18  16  26
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              25               311
  R1               4                18
  R2               1                16
  RX               3                26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     1
  7P LOSS WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7P LOSS MUTATED                          12
  7P LOSS WILD-TYPE                        61
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7P LOSS MUTATED                                           1    21
  7P LOSS WILD-TYPE                                         8   334
D53V6, multiclass
                                           clus
vv                                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                              12                61
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  21               334
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  24
  7P LOSS WILD-TYPE  12 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   24
  7P LOSS WILD-TYPE   12  312
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              24               312
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    31   6
  7Q LOSS WILD-TYPE 392  54
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               37               446 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                54 
$`7Q LOSS MUTATED`
TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AX-A1CA TCGA-AX-A1CR 
       19.96        91.04         1.18         0.49        20.28        11.08 
TCGA-AX-A2HK TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A11I TCGA-BG-A0M6 TCGA-BG-A0YV 
        2.96        80.38        17.85        75.72         7.92        12.56 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A15V 
        6.81        10.22        10.16        24.13        67.20        39.48 
TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QY 
       18.67         2.07        44.88         4.11        35.38        91.96 
TCGA-E6-A1LZ TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A212 TCGA-EY-A2ON 
       48.36        19.40        22.26         4.54         3.62        13.45 
TCGA-EY-A2OO TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       45.76        96.69        59.01        25.02        26.01        41.06 
TCGA-PG-A5BC 
       10.82 

$`7Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        23.21        68.65        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33        14.96         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        0.85         2.40         3.02         1.12         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        0.92        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       39.42        57.80        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        18.25        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       67.50        25.12        36.39         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        27.32        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.10         0.33         0.13         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       15.29        12.79        62.14         5.03        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        28.54        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        35.67        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
       34.98         6.21        31.76        24.99        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         1.41         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02         6.77         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU 
       41.42         8.48         0.26         4.27        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       36.62        24.30         9.37        12.39        31.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU 
       27.12        32.28        24.79        32.38        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 
       35.15        12.89        27.16        26.96        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 
        8.55         6.48        19.33        12.59        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       22.82        31.04        29.10        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       34.98        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
        9.07        28.93        28.96         1.74        13.15         2.43 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.49              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            96.69            191.84 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            19.96             23.11 
[1] "0.5 - 96.7 (20.0)"  "0.0 - 191.8 (23.1)"
[1] "hr=" "1.4"
D54V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  7Q LOSS MUTATED                                         8
  7Q LOSS WILD-TYPE                                     359
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  7Q LOSS MUTATED                               2
  7Q LOSS WILD-TYPE                            18
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  7Q LOSS MUTATED                                  27
  7Q LOSS WILD-TYPE                                71
D54V3, multiclass
                                         clus
vv                                        7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               8               359
  MIXED SEROUS AND ENDOMETRIOID                         2                18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    27                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     8  29
  7Q LOSS WILD-TYPE 130 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      8   29
  7Q LOSS WILD-TYPE  130  318
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                8               130
  YES              29               318
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    24   2   2   4
  7Q LOSS WILD-TYPE 312  20  15  25
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              24               312
  R1               2                20
  R2               2                15
  RX               4                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     0
  7Q LOSS WILD-TYPE                                4    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  7Q LOSS MUTATED                           9
  7Q LOSS WILD-TYPE                        64
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  7Q LOSS MUTATED                                           1    23
  7Q LOSS WILD-TYPE                                         8   332
D54V6, multiclass
                                           clus
vv                                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                               9                64
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  23               332
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  27
  7Q LOSS WILD-TYPE  12 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   27
  7Q LOSS WILD-TYPE   12  309
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              27               309
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    57  12
  8P LOSS WILD-TYPE 366  48
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               69               414 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               12                48 
$`8P LOSS MUTATED`
TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A3NF TCGA-AJ-A3TW 
       36.33        46.32        28.64         1.18         1.35         1.71 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LF TCGA-AP-A1DQ 
       57.80        45.53        36.89        48.79         3.39        41.95 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CC TCGA-AX-A1CN 
        0.56        37.78        16.96        13.55        12.43        25.12 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN 
       36.39        71.24        19.36         0.03         0.13        80.38 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 
       17.85         4.11        75.72       102.31        11.87        12.79 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MT TCGA-BG-A0YU 
        5.03        34.13         7.92        36.49        21.17        14.83 
TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A16G 
        6.81        10.16        24.13        29.95        22.55        27.42 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QT 
       13.22         0.72        44.88         4.11        35.38        12.39 
TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GS 
       91.96         7.99        32.38        22.26        23.90        15.09 
TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       15.81         3.62        14.40        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       17.92        36.00        96.69        59.01         9.07        28.93 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-PG-A5BC 
       41.06         1.74        10.82 

$`8P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        9.60         8.02        91.04         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
       14.96         1.08         1.97         0.39        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40         3.02         0.49         1.12         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
        0.92        36.99        20.65        15.62         0.76         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
       15.95         1.87        16.87         2.33        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N 
        5.95        23.31        86.07         8.22        39.42         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.20        20.91       125.42       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       33.73        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 
       67.50        11.08         4.77        30.12        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       68.71        33.40        40.50        26.33        17.75        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.13         0.20        20.52         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        8.35        14.47        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        23.01        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      191.84        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        34.98        38.37        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YV TCGA-BG-A186 
       34.29        28.54        52.83        56.58        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        35.67        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       34.98         6.21        10.22        31.76        24.99        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        67.20        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ 
       49.55        63.16        66.48        16.83        19.79         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        23.93         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.36        37.51        36.79        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY 
       24.30         2.33        22.92         1.41        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU 
       41.42         8.48         0.26         4.27        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       36.62        24.30         9.37        31.10        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       32.28        24.79        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        26.96        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       17.62        16.11        12.43         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       12.59        18.87        22.82        13.45        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       29.10         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 
       34.98        33.99         7.99        13.84         8.98        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-QS-A5YQ TCGA-QS-A5YR 
       25.02        26.01        13.15         2.43         4.21         5.52 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.03              0.10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           102.31            191.84 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            19.36             23.26 
[1] "0.0 - 102.3 (19.4)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.7"
D55V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8P LOSS MUTATED                                        15
  8P LOSS WILD-TYPE                                     352
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8P LOSS MUTATED                               4
  8P LOSS WILD-TYPE                            16
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8P LOSS MUTATED                                  50
  8P LOSS WILD-TYPE                                48
D55V3, multiclass
                                         clus
vv                                        8P LOSS MUTATED 8P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              15               352
  MIXED SEROUS AND ENDOMETRIOID                         4                16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    50                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    19  50
  8P LOSS WILD-TYPE 119 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     19   50
  8P LOSS WILD-TYPE  119  297
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               19               119
  YES              50               297
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED    43   4   3   7
  8P LOSS WILD-TYPE 293  18  14  22
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              43               293
  R1               4                18
  R2               3                14
  RX               7                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1     1
  8P LOSS WILD-TYPE                                3    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8P LOSS MUTATED                          18
  8P LOSS WILD-TYPE                        55
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8P LOSS MUTATED                                           0    46
  8P LOSS WILD-TYPE                                         9   309
D55V6, multiclass
                                           clus
vv                                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                              18                55
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  46               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"
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     1  47
  8P LOSS WILD-TYPE  12 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1   47
  8P LOSS WILD-TYPE   12  289
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              47               289
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    19   2
  8Q LOSS WILD-TYPE 404  58
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               21               462 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                58 
$`8Q LOSS MUTATED`
TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AP-A05D TCGA-AX-A1C7 TCGA-AX-A2H5 TCGA-AX-A2HF 
       46.32         1.18        57.80        16.96        71.24        19.36 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0KB TCGA-B5-A3S1 TCGA-BG-A0YU TCGA-BG-A3PP 
        0.13        80.38         4.11         5.03        14.83         6.81 
TCGA-BK-A26L TCGA-DI-A1NN TCGA-DI-A2QT TCGA-EO-A3KU TCGA-EY-A3L3 TCGA-EY-A3QX 
       24.13        35.38        12.39        22.26        27.35        13.84 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EY 
       36.00        96.69        28.93 

$`8Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33         9.60         8.02        91.04        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33        14.96         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79         0.85         2.40         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        39.42        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        16.24        18.25        33.73         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.10         0.33         0.13         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.03         0.13         0.23         1.18         8.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD 
       11.87        15.29        12.79        62.14        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98         7.92        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YV 
       16.34        34.29        28.54        52.83        56.58        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         1.41         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02         6.77         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
        4.11        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10        91.96        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        6.67        16.01         7.36        16.80        10.92         7.99 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.78        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       24.79        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        26.96        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
        8.55         6.48        19.33        12.59         3.62        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        13.45        45.76        31.04        29.10 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
        6.44        17.92         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        34.98        33.99         7.99        13.84         8.98 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       59.01         9.07        28.96        25.02        26.01        41.06 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74        13.15         2.43        10.82         4.21         5.52 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.13              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            96.69            191.84 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            22.26             22.87 
[1] "0.1 - 96.7 (22.3)"  "0.0 - 191.8 (22.9)"
[1] "hr=" "1.3"
D56V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  8Q LOSS MUTATED                                         2
  8Q LOSS WILD-TYPE                                     365
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  8Q LOSS MUTATED                               1
  8Q LOSS WILD-TYPE                            19
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  8Q LOSS MUTATED                                  18
  8Q LOSS WILD-TYPE                                80
D56V3, multiclass
                                         clus
vv                                        8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               2               365
  MIXED SEROUS AND ENDOMETRIOID                         1                19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    18                80
[1] 3 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, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     5  16
  8Q LOSS WILD-TYPE 133 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5   16
  8Q LOSS WILD-TYPE  133  331
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                5               133
  YES              16               331
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    12   1   1   2
  8Q LOSS WILD-TYPE 324  21  16  27
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              12               324
  R1               1                21
  R2               1                16
  RX               2                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  1     0
  8Q LOSS WILD-TYPE                                3    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  8Q LOSS MUTATED                           5
  8Q LOSS WILD-TYPE                        68
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  8Q LOSS MUTATED                                           0    13
  8Q LOSS WILD-TYPE                                         9   342
D56V6, multiclass
                                           clus
vv                                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                               5                68
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               0                 9
  WHITE                                                  13               342
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  14
  8Q LOSS WILD-TYPE  12 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   14
  8Q LOSS WILD-TYPE   12  322
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                12
  NOT HISPANIC OR LATINO              14               322
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    71  17
  9P LOSS WILD-TYPE 352  43
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               88               395 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               17                43 
$`9P LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GG TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0VP 
      149.56        87.32        36.82        19.96        17.59        42.35 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD 
       91.04        28.64         7.33         1.18         1.08         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.12         2.24         1.64        22.26         1.28         0.92 
TCGA-AJ-A3NH TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 
        0.76        21.99         5.95        57.80        45.53        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
      125.42        97.71        41.95        18.25        33.73         0.56 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR 
       37.78        16.96        13.55        76.83        36.39        11.08 
TCGA-AX-A2H4 TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0K8 
       30.12         0.13        20.52         0.13         0.13        17.85 
TCGA-B5-A0KB TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OE 
        4.11        36.82       102.31        11.87         5.03        34.95 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L 
        7.92        36.49        15.45        10.22        10.16        24.13 
TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 
       16.64        61.87        49.55        22.55        39.48        37.32 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-DI-A1NN TCGA-DI-A2QT 
       31.07        18.67        13.22         2.07        35.38        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3B1 
       31.10        91.96         7.99        32.38        27.16        26.96 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A214 
       16.34         4.54        15.09        15.81         3.62        14.40 
TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
        3.72        34.98        36.00         9.07        28.93        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-PG-A5BC 
       26.01        41.06        13.15        10.82 

$`9P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       19.59        24.62        29.06        15.95         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
       36.33         9.60         8.02        46.32         5.33         5.16 
TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.96         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
        3.02         0.76         1.68        14.66        22.49        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
       16.87         1.71         2.33        83.67        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        39.42        36.89         7.86        12.20        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       31.30        35.54        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       27.85        16.24        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        28.54        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       19.20        15.25        20.28        12.43        20.05        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 
       54.12        67.50        25.12         4.77        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.10         0.33         0.20         0.03         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        8.35        14.47        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       15.29        12.79        62.14        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        34.98        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.76        24.99        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ 
       23.47        85.55        78.21         4.80        77.95        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        67.20        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
        8.55         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        21.99        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O 
       37.51        36.79        27.42        11.51        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27         4.11        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       36.62        24.30         9.37        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.78        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       22.26         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.88        17.62        16.11        12.43 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM 
        8.55         6.48        19.33        12.59        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       13.45        45.76        31.04        29.10        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX 
        6.44        17.92         2.14         6.97         5.29        40.01 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       33.99         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-QS-A5YQ TCGA-QS-A5YR 
       28.96         1.74         2.43         4.21         5.52 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.13              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           149.56            191.84 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           19.315            23.340 
[1] "0.1 - 149.6 (19.3)" "0.0 - 191.8 (23.3)"
[1] "hr=" "1.9"
D57V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9P LOSS MUTATED                                        30
  9P LOSS WILD-TYPE                                     337
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9P LOSS MUTATED                               8
  9P LOSS WILD-TYPE                            12
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9P LOSS MUTATED                                  51
  9P LOSS WILD-TYPE                                47
D57V3, multiclass
                                         clus
vv                                        9P LOSS MUTATED 9P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              30               337
  MIXED SEROUS AND ENDOMETRIOID                         8                12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    51                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    22  67
  9P LOSS WILD-TYPE 116 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     22   67
  9P LOSS WILD-TYPE  116  280
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               22               116
  YES              67               280
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    55   5   7   8
  9P LOSS WILD-TYPE 281  17  10  21
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              55               281
  R1               5                17
  R2               7                10
  RX               8                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  1     2
  9P LOSS WILD-TYPE                                3    17
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9P LOSS MUTATED                          17
  9P LOSS WILD-TYPE                        56
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9P LOSS MUTATED                                           2    62
  9P LOSS WILD-TYPE                                         7   293
D57V6, multiclass
                                           clus
vv                                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   2                17
  BLACK OR AFRICAN AMERICAN                              17                56
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  62               293
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2  63
  9P LOSS WILD-TYPE  11 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2   63
  9P LOSS WILD-TYPE   11  273
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO              63               273
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    86  19
  9Q LOSS WILD-TYPE 337  41
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              105               378 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               19                41 
$`9Q LOSS MUTATED`
TCGA-A5-A0GG TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A2K2 
       87.32        36.82        19.96        17.59        42.35        91.04 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3BD 
       28.64         7.33         1.18         0.39         2.40         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.12         2.24         1.64        22.26         1.28         0.92 
TCGA-AJ-A3NH TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 
        0.76        21.99         5.95        57.80        45.53        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B 
      125.42        97.71        18.25        33.73         0.56        53.92 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 
       37.78        16.96        76.83        36.39        11.08        30.12 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3G1 
       61.18        19.36         2.96         0.23         0.13        20.52 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I 
        0.13         0.13        80.38        17.85         4.11        75.72 
TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OE 
       36.82       102.31        50.89        11.87         5.03        34.95 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC 
        7.92        36.49        12.56        15.45         1.81        10.22 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZQ 
       10.16        24.13        16.64        61.87        49.55         8.55 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V 
       22.55        39.48        37.32        31.07        18.67         1.41 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN 
       28.08        13.22         2.07        44.88         4.11        35.38 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG 
       31.10        91.96        48.36         7.99        10.78        32.38 
TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GS 
       19.40        27.16        26.96        16.34         4.54        15.09 
TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ 
       15.81        12.59         3.62        14.40        13.45        29.10 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       34.98        36.00         9.07        28.93        25.02        26.01 
TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-PG-A5BC 
       41.06        13.15        10.82 

$`9Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
        3.22       105.37        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF 
       68.65        19.59        24.62        29.06        15.95         7.92 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 
       11.44        36.33         9.60         8.02        46.32         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM 
        5.16        14.96         1.08         1.97        19.79         0.85 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
        3.02         0.76         1.68        14.66        22.49        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
       16.87         1.71         2.33        83.67        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        39.42        36.89         7.86        12.20        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       10.42        27.85        16.24        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       34.98        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        28.54        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       19.20        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 
       72.56        54.12        67.50        25.12         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       33.53        68.71        33.40        40.50        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       27.32        31.13        38.70         0.10         0.33         0.20 
TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.03         0.23         1.18         8.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        11.01         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        54.44        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       17.36        16.57       191.84        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       15.29        12.79        62.14        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        34.98        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
        6.81        35.90        34.98         6.21        31.76        24.99 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        19.79        29.95         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93         1.74         4.44        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X 
       11.51        29.92        33.63        10.65         0.69         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        8.48         0.26         4.27        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       24.30         9.37        12.39        23.38        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R 
        6.67        16.01         7.36        16.80        10.92        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS 
       35.05        33.01        27.12        32.28        24.79        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 
       19.36        35.15        12.89        22.26         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       17.62        16.11        12.43         8.55         6.48        19.33 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       18.87        22.82        45.76        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
        6.44        17.92         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       40.01        33.99         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-QS-A5YQ TCGA-QS-A5YR 
       59.01        28.96         1.74         2.43         4.21         5.52 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.13              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           125.42            191.84 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            19.36             23.36 
[1] "0.1 - 125.4 (19.4)" "0.0 - 191.8 (23.4)"
[1] "hr=" "1.9"
D58V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  9Q LOSS MUTATED                                        42
  9Q LOSS WILD-TYPE                                     325
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  9Q LOSS MUTATED                               9
  9Q LOSS WILD-TYPE                            11
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  9Q LOSS MUTATED                                  55
  9Q LOSS WILD-TYPE                                43
D58V3, multiclass
                                         clus
vv                                        9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              42               325
  MIXED SEROUS AND ENDOMETRIOID                         9                11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    55                43
[1] 3 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, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    25  81
  9Q LOSS WILD-TYPE 113 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     25   81
  9Q LOSS WILD-TYPE  113  266
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               25               113
  YES              81               266
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    68   4   7   8
  9Q LOSS WILD-TYPE 268  18  10  21
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              68               268
  R1               4                18
  R2               7                10
  RX               8                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     1
  9Q LOSS WILD-TYPE                                4    18
                   vv
clus                BLACK OR AFRICAN AMERICAN
  9Q LOSS MUTATED                          21
  9Q LOSS WILD-TYPE                        52
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  9Q LOSS MUTATED                                           2    75
  9Q LOSS WILD-TYPE                                         7   280
D58V6, multiclass
                                           clus
vv                                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        0                 4
  ASIAN                                                   1                18
  BLACK OR AFRICAN AMERICAN                              21                52
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               2                 7
  WHITE                                                  75               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"
D58V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     2  75
  9Q LOSS WILD-TYPE  11 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      2   75
  9Q LOSS WILD-TYPE   11  261
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                11
  NOT HISPANIC OR LATINO              75               261
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    27   7
  10P LOSS WILD-TYPE 396  53
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                34                449 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                 53 
$`10P LOSS MUTATED`
TCGA-A5-A1OH TCGA-AJ-A3BF TCGA-AJ-A3NF TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L9 
       36.33         1.12         1.35        21.99        45.53       125.42 
TCGA-AP-A0LI TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       97.71        33.73        53.92        36.39        11.08         4.77 
TCGA-AX-A2HK TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0KB TCGA-BG-A0M8 
        2.96        20.52         0.13         0.13         4.11        36.49 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A16I TCGA-DI-A1NN 
       15.45         6.81        24.13        67.20        11.51        35.38 
TCGA-E6-A1LZ TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2OQ 
       48.36        27.16        16.34        17.62        15.09        29.10 
TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A3PV TCGA-K6-A3WQ 
       36.00        28.93        41.06        13.15 

$`10P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.16         7.33        14.96         1.18         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79         0.85         2.40         3.02         0.49 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.26         1.28         0.92        36.99        20.65        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
        0.76         1.94        15.95         1.87        16.87         1.71 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        2.33        83.67         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       39.42        57.80        36.89         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO 
       30.90        10.42        27.85        16.24        18.25         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 
       72.56        54.12        67.50        25.12        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        27.32        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 
        0.10         0.33         0.13         0.20         0.03         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18         8.35        14.47        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       12.79        62.14         5.03        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
        6.21        10.22        10.16        31.76        24.99        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       24.30         9.37        12.39        31.10        91.96        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       27.12        32.28        24.79        32.38        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 
       19.36        35.15        12.89        26.96        22.26         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        17.88        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59         3.62        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        13.45        45.76        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
        6.44        17.92         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        34.98        33.99         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       96.69        59.01         9.07        28.96        25.02        26.01 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74         2.43        10.82         4.21         5.52 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.13               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            125.42             191.84 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             23.06              22.82 
[1] "0.1 - 125.4 (23.1)" "0.0 - 191.8 (22.8)"
[1] "hr=" "1.7"
D59V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10P LOSS MUTATED                                         9
  10P LOSS WILD-TYPE                                     358
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10P LOSS MUTATED                               4
  10P LOSS WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10P LOSS MUTATED                                  21
  10P LOSS WILD-TYPE                                77
D59V3, multiclass
                                         clus
vv                                        10P LOSS MUTATED 10P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                9                358
  MIXED SEROUS AND ENDOMETRIOID                          4                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     21                 77
[1] 3 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, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     7  27
  10P LOSS WILD-TYPE 131 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7   27
  10P LOSS WILD-TYPE  131  320
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 7                131
  YES               27                320
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    20   2   3   4
  10P LOSS WILD-TYPE 316  20  14  25
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               20                316
  R1                2                 20
  R2                3                 14
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     0
  10P LOSS WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10P LOSS MUTATED                          10
  10P LOSS WILD-TYPE                        63
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10P LOSS MUTATED                                           2    20
  10P LOSS WILD-TYPE                                         7   335
D59V6, multiclass
                                           clus
vv                                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                               10                 63
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   20                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"
D59V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     0  24
  10P LOSS WILD-TYPE  13 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0   24
  10P LOSS WILD-TYPE   13  312
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO               24                312
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    27   6
  10Q LOSS WILD-TYPE 396  54
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                33                450 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                 54 
$`10Q LOSS MUTATED`
TCGA-A5-A1OH TCGA-AJ-A3BF TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LI 
       36.33         1.12         1.71        45.53       125.42        97.71 
TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-AX-A3G1 
       33.73        53.92        11.08         4.77         2.96        20.52 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0KB TCGA-B5-A1MS TCGA-BG-A0M8 TCGA-BG-A18C 
        0.13         0.13         4.11       102.31        36.49        15.45 
TCGA-BG-A3PP TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A17K TCGA-D1-A3DH 
        6.81        67.20        11.51        29.92        28.08         4.11 
TCGA-DI-A1NN TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GR TCGA-FI-A2D2 TCGA-FI-A2EU 
       35.38        27.16        16.34        17.62        36.00        96.69 
TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KJ-A3U4 
       41.06        13.15         2.43 

$`10Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.16         7.33        14.96         1.18         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79         0.85         2.40         3.02         0.49 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.33        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        57.80        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91        48.79       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D 
       46.45        35.34        45.99        66.58        34.98        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       40.50        19.36        26.33        17.75        27.32        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       38.70         0.23         0.10         0.33         0.13         0.20 
TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN 
        0.03         0.23         1.18         8.35        14.47        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      191.84        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       15.29        12.79        62.14         5.03        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98         7.92        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        35.67        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       27.42        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02         6.77         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        0.26         4.27        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10        91.96        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       27.12        32.28        24.79        32.38        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 
       19.36        35.15        12.89        26.96        22.26         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.88        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
        8.55         6.48        19.33        12.59         3.62        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        13.45        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84         6.44        17.92         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        3.72         5.29        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
       13.84         8.98        59.01         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       25.02        26.01         1.74        10.82         4.21         5.52 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.13               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            125.42             191.84 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             20.52              22.87 
[1] "0.1 - 125.4 (20.5)" "0.0 - 191.8 (22.9)"
[1] "hr=" "1.5"
D60V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  10Q LOSS MUTATED                                        11
  10Q LOSS WILD-TYPE                                     356
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  10Q LOSS MUTATED                               4
  10Q LOSS WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  10Q LOSS MUTATED                                  18
  10Q LOSS WILD-TYPE                                80
D60V3, multiclass
                                         clus
vv                                        10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               11                356
  MIXED SEROUS AND ENDOMETRIOID                          4                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     18                 80
[1] 3 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, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     6  27
  10Q LOSS WILD-TYPE 132 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6   27
  10Q LOSS WILD-TYPE  132  320
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 6                132
  YES               27                320
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    22   1   1   4
  10Q LOSS WILD-TYPE 314  21  16  25
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               22                314
  R1                1                 21
  R2                1                 16
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     0
  10Q LOSS WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  10Q LOSS MUTATED                           7
  10Q LOSS WILD-TYPE                        66
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  10Q LOSS MUTATED                                           2    21
  10Q LOSS WILD-TYPE                                         7   334
D60V6, multiclass
                                           clus
vv                                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                7                 66
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   21                334
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  23
  10Q LOSS WILD-TYPE  12 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   23
  10Q LOSS WILD-TYPE   12  313
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               23                313
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    51  13
  11P LOSS WILD-TYPE 372  47
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                64                419 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                 47 
$`11P LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       65.75        60.53        36.82        11.44        36.33        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       46.32        28.64         1.18         0.49         1.12         2.24 
TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AP-A05A TCGA-AP-A0LF 
        1.64         1.35         0.76        16.87        39.42         3.39 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A1CA TCGA-AX-A1CR 
       41.95        18.25        33.73        53.92        20.28        11.08 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 
       20.52         0.03         0.13         0.13        23.01        17.85 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A5OD TCGA-BG-A0YV 
       36.82        32.09       102.31        12.79        34.13        12.56 
TCGA-BK-A139 TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A1O0 
       10.16        16.64        22.55        18.67        18.25         2.07 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-EO-A1Y8 
        4.27         4.11         9.37        12.39        31.10        10.78 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       19.40        34.39        19.27        18.84        17.62        15.09 
TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EY 
       14.40        45.76        27.35         3.72        36.00        28.93 
TCGA-FI-A2F8 TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC 
       25.02        13.15         2.43        10.82 

$`11P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K5 TCGA-A5-A2K7 
       15.95         7.92         9.60         8.02         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33        14.96         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
        0.85         2.40         3.02         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26         1.28         0.92        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW 
       15.62         1.94        15.95         1.87         1.71         2.33 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S 
       30.90        10.42        27.85        16.24         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       67.50        25.12        36.39         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 
        0.23         0.10         0.33         0.13         0.20         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18         8.35        14.47        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.34        30.51        25.91        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11R 
       75.72        54.44        45.90        43.96        40.50        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE 
       11.87        15.29        62.14         5.03        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        28.54        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        35.67        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98         6.21        10.22        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        67.20        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02         6.77         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
       13.22         0.72        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QY 
       16.31        39.29        36.62        24.30        35.38        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92         7.99        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AU 
       33.01        27.12        32.28        24.79        32.38        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        12.89        27.16        26.96        22.26        16.34 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       17.88        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       19.33        12.59         3.62        18.87        22.82        13.45 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       31.04        29.10        13.84         6.44        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        6.97         5.29        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 
       13.84         8.98        96.69        59.01         9.07        28.96 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-QS-A5YQ TCGA-QS-A5YR 
       26.01        41.06         1.74         4.21         5.52 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.03               0.10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            102.31             191.84 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             18.05              23.70 
[1] "0.0 - 102.3 (18.1)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2.4"
D61V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11P LOSS MUTATED                                        23
  11P LOSS WILD-TYPE                                     344
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11P LOSS MUTATED                               6
  11P LOSS WILD-TYPE                            14
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11P LOSS MUTATED                                  36
  11P LOSS WILD-TYPE                                62
D61V3, multiclass
                                         clus
vv                                        11P LOSS MUTATED 11P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               23                344
  MIXED SEROUS AND ENDOMETRIOID                          6                 14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     36                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    11  54
  11P LOSS WILD-TYPE 127 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     11   54
  11P LOSS WILD-TYPE  127  293
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                11                127
  YES               54                293
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    38   3   4   5
  11P LOSS WILD-TYPE 298  19  13  24
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               38                298
  R1                3                 19
  R2                4                 13
  RX                5                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  1     1
  11P LOSS WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11P LOSS MUTATED                          16
  11P LOSS WILD-TYPE                        57
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11P LOSS MUTATED                                           1    43
  11P LOSS WILD-TYPE                                         8   312
D61V6, multiclass
                                           clus
vv                                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                               16                 57
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   43                312
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  46
  11P LOSS WILD-TYPE  11 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   46
  11P LOSS WILD-TYPE   11  290
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               46                290
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    49  12
  11Q LOSS WILD-TYPE 374  48
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                61                422 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                12                 48 
$`11Q LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       65.75        60.53        36.82        11.44        36.33        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF 
       46.32        28.64         1.18         0.85         0.49         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A0LF 
        2.24         1.64         0.76        16.87         1.71         3.39 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A1CR TCGA-AX-A2IO TCGA-AX-A3G1 TCGA-AX-A3G3 
       18.25        33.73        11.08        38.70        20.52         0.03 
TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A1MS 
        0.13        23.01        17.85        36.82        32.09       102.31 
TCGA-B5-A5OD TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A169 
       34.13        12.56         6.81        16.64        22.55        37.32 
TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A3DG TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       18.67        18.25         4.27        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EY-A1GO TCGA-EY-A1GP 
       31.10        10.78        19.40        22.26        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2OO 
       17.62        15.09         8.55        12.59        14.40        45.76 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-K6-A3WQ 
       27.35         6.44         3.72        36.00        96.69        13.15 
TCGA-KJ-A3U4 
        2.43 

$`11Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K5 TCGA-A5-A2K7 
       15.95         7.92         9.60         8.02         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33        14.96         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        2.40         3.02         0.76         1.68        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AP-A051 
       15.62         1.94        15.95         1.87         2.33        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO 
        6.71        30.90        10.42        27.85        16.24         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
        2.96        31.13         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.13         0.23         1.18         8.35        14.47 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       43.96        40.50        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       191.84        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14         5.03        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
       10.22        10.16        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        23.93         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         1.41         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02         6.77         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY 
        2.33        22.92         1.41        13.22         0.72        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DI-A0WH 
       41.42         8.48        44.88         0.26         4.11        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
       39.29        36.62        24.30        91.96        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92         7.99        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       32.28        24.79        32.38        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        26.96        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GT 
       23.90        22.78        13.97         6.90        17.88        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 
       12.43        15.81         6.48        19.33         3.62        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 
       22.82        13.45        31.04        29.10        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        2.14         6.97         5.29        40.01        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        13.84         8.98        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-PG-A5BC 
       28.96        25.02        26.01        41.06         1.74        10.82 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.03               0.10 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            102.31             191.84 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             17.85              23.80 
[1] "0.0 - 102.3 (17.9)" "0.1 - 191.8 (23.8)"
[1] "hr=" "2.2"
D62V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  11Q LOSS MUTATED                                        20
  11Q LOSS WILD-TYPE                                     347
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  11Q LOSS MUTATED                               7
  11Q LOSS WILD-TYPE                            13
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  11Q LOSS MUTATED                                  35
  11Q LOSS WILD-TYPE                                63
D62V3, multiclass
                                         clus
vv                                        11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               20                347
  MIXED SEROUS AND ENDOMETRIOID                          7                 13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     35                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     8  54
  11Q LOSS WILD-TYPE 130 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      8   54
  11Q LOSS WILD-TYPE  130  293
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 8                130
  YES               54                293
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    36   4   4   6
  11Q LOSS WILD-TYPE 300  18  13  23
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               36                300
  R1                4                 18
  R2                4                 13
  RX                6                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  1     1
  11Q LOSS WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  11Q LOSS MUTATED                          15
  11Q LOSS WILD-TYPE                        58
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  11Q LOSS MUTATED                                           0    41
  11Q LOSS WILD-TYPE                                         9   314
D62V6, multiclass
                                           clus
vv                                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                               15                 58
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   41                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"
D62V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3  44
  11Q LOSS WILD-TYPE  10 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   44
  11Q LOSS WILD-TYPE   10  292
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               44                292
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    28  11
  12P LOSS WILD-TYPE 395  49
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                39                444 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                11                 49 
$`12P LOSS MUTATED`
TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-AJ-A2QM TCGA-AJ-A3BI TCGA-AJ-A3EM 
       19.96        91.04        28.64         0.85         2.24        22.26 
TCGA-AJ-A3NF TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 
        1.35        21.99        45.53        97.71        33.40        18.25 
TCGA-AX-A06B TCGA-AX-A2H4 TCGA-AX-A3FX TCGA-B5-A0K3 TCGA-B5-A1MS TCGA-B5-A3S1 
       53.92        30.12         0.13        23.01       102.31         5.03 
TCGA-B5-A5OE TCGA-BG-A0YV TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0V8 TCGA-D1-A0ZZ 
       34.95        12.56        10.16        16.64        49.55        22.55 
TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-EO-A3B1 TCGA-EO-A3KW 
       39.48        18.67        44.88         4.11        26.96        16.34 
TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A 
       15.09         8.55         3.62        29.10         6.44         3.72 
TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A3PV 
       96.69         9.07        41.06 

$`12P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        23.21        68.65        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        9.60         8.02        46.32         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK 
        2.40         3.02         0.49         1.12         0.76         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
        1.64        14.66        22.49         1.28         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        15.62         0.76         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 
       16.87         1.71         2.33        83.67         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        39.42        57.80        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       33.73         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       36.39        11.08         4.77        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.33         0.20        20.52         0.03         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18         8.35        14.47         0.13        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       12.79        62.14        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
        6.21        10.22        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU 
       41.42         8.48         0.26         4.27        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       36.62        24.30        35.38         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       91.96        23.38        48.36        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.01         7.36        16.80        10.92         7.99        10.78 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        32.28        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.38        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       27.16        22.26         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       13.97         6.90        19.27        18.84        17.88        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        15.81         6.48        19.33        12.59 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        13.45        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       27.35        13.84        17.92         2.14         6.97         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        34.98        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
        8.98        59.01        28.93        28.96        25.02        26.01 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74        13.15         2.43        10.82         4.21         5.52 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.13               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            102.31             191.84 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             21.99              23.26 
[1] "0.1 - 102.3 (22.0)" "0.0 - 191.8 (23.3)"
[1] "hr=" "2.7"
D63V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12P LOSS MUTATED                                        13
  12P LOSS WILD-TYPE                                     354
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12P LOSS MUTATED                               1
  12P LOSS WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12P LOSS MUTATED                                  25
  12P LOSS WILD-TYPE                                73
D63V3, multiclass
                                         clus
vv                                        12P LOSS MUTATED 12P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               13                354
  MIXED SEROUS AND ENDOMETRIOID                          1                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     25                 73
[1] 3 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, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     7  32
  12P LOSS WILD-TYPE 131 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      7   32
  12P LOSS WILD-TYPE  131  315
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 7                131
  YES               32                315
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    24   3   4   3
  12P LOSS WILD-TYPE 312  19  13  26
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               24                312
  R1                3                 19
  R2                4                 13
  RX                3                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     0
  12P LOSS WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12P LOSS MUTATED                           9
  12P LOSS WILD-TYPE                        64
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12P LOSS MUTATED                                           1    25
  12P LOSS WILD-TYPE                                         8   330
D63V6, multiclass
                                           clus
vv                                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                9                 64
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   25                330
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  27
  12P LOSS WILD-TYPE  12 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   27
  12P LOSS WILD-TYPE   12  309
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               27                309
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    22   9
  12Q LOSS WILD-TYPE 401  51
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                31                452 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                 51 
$`12Q LOSS MUTATED`
TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH 
       19.96        91.04        28.64         0.92         1.35         0.76 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-B5-A0K3 
       21.99        45.53        97.71        33.40        18.25        23.01 
TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0YV TCGA-BK-A139 TCGA-BK-A4ZD TCGA-D1-A0ZZ 
        5.03        34.95        12.56        10.16        16.64        22.55 
TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A3DH TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GW 
       39.48        18.67         4.11        26.96        16.34         8.55 
TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2EU TCGA-FI-A2EX 
        3.62        29.10         6.44         3.72        96.69         9.07 
TCGA-FI-A3PV 
       41.06 

$`12Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        23.21        68.65        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        9.60         8.02        46.32         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.85         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        2.24         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
        1.28        36.99        20.65        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A053 
        1.87        16.87         1.71         2.33        83.67         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J 
       23.31        86.07         8.22        39.42        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       27.12        82.52        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        33.73         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        27.32         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       38.70         0.23         0.10         0.33         0.13         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.03         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       14.47         0.13        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       10.22        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH 
       41.42         8.48        44.88         0.26         4.27        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10        91.96        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        6.67        16.01         7.36        16.80        10.92         7.99 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.78        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       24.79        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       12.89        27.16        22.26         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        15.09        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       19.33        12.59        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 
       45.76        31.04        27.35        13.84        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
        6.97         5.29        40.01        34.98        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F4 
        7.99        13.84         8.98        59.01        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC 
       25.02        26.01         1.74        13.15         2.43        10.82 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.76               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             97.71             191.84 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            18.670             23.325 
[1] "0.8 - 97.7 (18.7)"  "0.0 - 191.8 (23.3)"
[1] "hr=" "3.2"
D64V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  12Q LOSS MUTATED                                         8
  12Q LOSS WILD-TYPE                                     359
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  12Q LOSS MUTATED                               1
  12Q LOSS WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  12Q LOSS MUTATED                                  22
  12Q LOSS WILD-TYPE                                76
D64V3, multiclass
                                         clus
vv                                        12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                8                359
  MIXED SEROUS AND ENDOMETRIOID                          1                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     22                 76
[1] 3 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, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     6  25
  12Q LOSS WILD-TYPE 132 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      6   25
  12Q LOSS WILD-TYPE  132  322
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 6                132
  YES               25                322
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    22   2   2   2
  12Q LOSS WILD-TYPE 314  20  15  27
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               22                314
  R1                2                 20
  R2                2                 15
  RX                2                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     0
  12Q LOSS WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  12Q LOSS MUTATED                           8
  12Q LOSS WILD-TYPE                        65
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  12Q LOSS MUTATED                                           0    19
  12Q LOSS WILD-TYPE                                         9   336
D64V6, multiclass
                                           clus
vv                                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                8                 65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                   19                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"
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  20
  12Q LOSS WILD-TYPE  12 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   20
  12Q LOSS WILD-TYPE   12  316
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               20                316
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    61  14
  13Q LOSS WILD-TYPE 362  46
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                75                408 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                 46 
$`13Q LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A2K2 TCGA-A5-A3LO 
      149.56        60.53        17.59        42.35        91.04         7.33 
TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       14.96         0.39         0.85         2.24         1.64        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A05P TCGA-AP-A0LI 
        1.28         0.76         1.71        45.53        20.91        97.71 
TCGA-AP-A0LO TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1C9 TCGA-AX-A1CK 
       33.40        33.73         0.56        53.92        15.25        67.50 
TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3G1 
       36.39        30.12         2.96        38.70         0.13        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0KB TCGA-B5-A11P 
        0.03         0.13         0.13        23.01         4.11        36.82 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A18C 
       11.87        12.79        34.95         7.92        12.56        15.45 
TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 
       23.70         6.81        10.16        16.64        61.87        67.20 
TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU 
       37.32        31.07         0.69         1.41         6.77        13.22 
TCGA-D1-A3DG TCGA-DI-A1NN TCGA-DI-A1NO TCGA-EO-A1Y7 TCGA-EO-A3AS TCGA-EO-A3AZ 
        4.27        35.38         9.37         7.99        34.39        27.16 
TCGA-EY-A1GC TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A2ON 
        4.54        18.84        17.62        15.81         8.55        13.45 
TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-FI-A2EX TCGA-FI-A2EY 
       45.76        29.10        13.84        17.92         9.07        28.93 
TCGA-FI-A2F8 TCGA-K6-A3WQ TCGA-KJ-A3U4 
       25.02        13.15         2.43 

$`13Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ 
       68.65        19.96        19.59        24.62        29.06        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
        7.92        11.44        36.33         9.60         8.02        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       28.64         5.33         5.16         1.18         1.08         1.97 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.68        14.66        22.49         0.92        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
        1.35        15.62         1.94        15.95         1.87        16.87 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.33        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        57.80        36.89         7.86        12.20 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       36.36        31.73        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S 
       30.90        10.42        27.85        16.24        18.25        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CN TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       25.12        11.08         4.77        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       27.32        31.13         0.23         0.10         0.33         0.20 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR 
        0.23         1.18         8.35        14.47        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A3S1 
       14.40        14.70        11.70        15.29        62.14         5.03 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.13        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
        9.57        35.67        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
        6.21        10.22        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        4.80        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        11.51        29.92        33.63        10.65 
TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
       18.67         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW 
       11.15        24.30         2.33        22.92         1.41         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT 
        4.11        16.31        39.29        36.62        24.30        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10        91.96        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 
        6.67        16.01         7.36        16.80        10.92        10.78 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        32.28        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 
       32.38        19.40        19.36        35.15        12.89        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       22.26        16.34         6.21        14.99         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
        6.90        19.27        17.88        15.09        16.11        12.43 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59         3.62        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 
       22.82        31.04        27.35         6.44         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
        3.72         5.29        40.01        34.98        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 
        7.99        13.84         8.98        96.69        59.01        28.96 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       26.01        41.06         1.74        10.82         4.21         5.52 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.03               0.10 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            149.56             191.84 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            15.450             23.915 
[1] "0.0 - 149.6 (15.4)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.1"
D65V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  13Q LOSS MUTATED                                        40
  13Q LOSS WILD-TYPE                                     327
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  13Q LOSS MUTATED                               5
  13Q LOSS WILD-TYPE                            15
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  13Q LOSS MUTATED                                  31
  13Q LOSS WILD-TYPE                                67
D65V3, multiclass
                                         clus
vv                                        13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               40                327
  MIXED SEROUS AND ENDOMETRIOID                          5                 15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     31                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V4, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    15  61
  13Q LOSS WILD-TYPE 123 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     15   61
  13Q LOSS WILD-TYPE  123  286
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                15                123
  YES               61                286
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    49   3   4   4
  13Q LOSS WILD-TYPE 287  19  13  25
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               49                287
  R1                3                 19
  R2                4                 13
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     2
  13Q LOSS WILD-TYPE                                4    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  13Q LOSS MUTATED                          14
  13Q LOSS WILD-TYPE                        59
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  13Q LOSS MUTATED                                           2    55
  13Q LOSS WILD-TYPE                                         7   300
D65V6, multiclass
                                           clus
vv                                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                               14                 59
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   55                300
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4  56
  13Q LOSS WILD-TYPE   9 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4   56
  13Q LOSS WILD-TYPE    9  280
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  9
  NOT HISPANIC OR LATINO               56                280
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    42  10
  14Q LOSS WILD-TYPE 381  50
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                52                431 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                10                 50 
$`14Q LOSS MUTATED`
TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K4 TCGA-AJ-A23M 
       60.53        19.96        17.59        11.44        28.64         1.18 
TCGA-AJ-A3BD TCGA-AJ-A3NH TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 
        0.49         0.76        45.53        36.89        48.79       125.42 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A3G1 TCGA-AX-A3G4 
       97.71        33.40        37.78        20.28        20.52         0.13 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0KB TCGA-B5-A11I 
        0.23         0.13        80.38        23.01         4.11        75.72 
TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C TCGA-BK-A0CC 
       36.82        11.87         5.03        34.13        15.45        10.22 
TCGA-BK-A139 TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-DI-A1NN 
       10.16        11.51         6.77        13.22         0.72        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW 
        9.37        12.39        32.38        34.39        22.26        16.34 
TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OQ 
       19.27        17.62        15.09        14.40        45.76        29.10 
TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2F9 TCGA-H5-A2HR 
        3.72        34.98        26.01         1.74 

$`14Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       23.21        68.65        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       15.95         7.92        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N 
       46.32         5.33         5.16         7.33        14.96         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76         2.24         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26         1.28         0.92        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
        1.35        15.62         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.71         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05N TCGA-AP-A05O 
       86.07         8.22        39.42        57.80         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.55        15.25        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.20         0.03         1.18         8.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        54.44        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A5OC 
       14.70        11.70        15.29        12.79        62.14        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98         7.92        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       12.56        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
        6.81        35.90        34.98         6.21        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        1.41        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       24.30        31.10        91.96        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.28        24.79        19.40        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       27.16        26.96         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97         6.90        18.84        17.88        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       15.81         8.55         6.48        19.33        12.59         3.62 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       18.87        22.82        13.45        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX 
        6.44        17.92         2.14         6.97         5.29        40.01 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV 
       59.01         9.07        28.93        28.96        25.02        41.06 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       13.15         2.43        10.82         4.21         5.52 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.13               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            125.42             191.84 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            18.445             23.340 
[1] "0.1 - 125.4 (18.4)" "0.0 - 191.8 (23.3)"
[1] "hr=" "1.9"
D66V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  14Q LOSS MUTATED                                        19
  14Q LOSS WILD-TYPE                                     348
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  14Q LOSS MUTATED                               3
  14Q LOSS WILD-TYPE                            17
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  14Q LOSS MUTATED                                  31
  14Q LOSS WILD-TYPE                                67
D66V3, multiclass
                                         clus
vv                                        14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               19                348
  MIXED SEROUS AND ENDOMETRIOID                          3                 17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     31                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V4, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    17  36
  14Q LOSS WILD-TYPE 121 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     17   36
  14Q LOSS WILD-TYPE  121  311
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                17                121
  YES               36                311
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED    30   2   3   3
  14Q LOSS WILD-TYPE 306  20  14  26
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               30                306
  R1                2                 20
  R2                3                 14
  RX                3                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  1     2
  14Q LOSS WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  14Q LOSS MUTATED                          17
  14Q LOSS WILD-TYPE                        56
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  14Q LOSS MUTATED                                           1    28
  14Q LOSS WILD-TYPE                                         8   327
D66V6, multiclass
                                           clus
vv                                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                               17                 56
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   28                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"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     3  30
  14Q LOSS WILD-TYPE  10 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3   30
  14Q LOSS WILD-TYPE   10  306
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               30                306
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    75  18
  15Q LOSS WILD-TYPE 348  42
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                93                390 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                18                 42 
$`15Q LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K2 
       65.75        60.53        19.96        17.59        11.44        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       46.32        28.64         7.33        14.96         1.18         1.08 
TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
        0.39         0.85         0.49         2.24         1.64        22.26 
TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A053 
        1.35         0.76        16.87         1.71        21.99         5.95 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A06B 
       45.53        48.79       125.42        18.25        33.73        53.92 
TCGA-AX-A0IW TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H2 
       37.78        15.25        20.28        12.43        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FZ TCGA-AX-A3G3 
       30.12        61.18         2.96         0.23         0.20         0.03 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB 
        0.23         0.13        80.38        23.01        17.85         4.11 
TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A18C TCGA-BG-A3PP 
       36.82       102.31        12.79         5.03        15.45         6.81 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A16I 
       16.64        67.20        49.55         8.55        22.55        11.51 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A3DH 
       31.07        18.67         1.41         6.77        13.22         4.11 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       91.96        48.36        10.78        32.38        19.40        34.39 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP 
       27.16        26.96        22.26         4.54        19.27        18.84 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ 
       12.59         3.62        14.40        13.45        45.76        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW 
       27.35         6.44        17.92        36.00        96.69        59.01 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-K6-A3WQ 
       25.02        26.01        13.15 

$`15Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       68.65        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K5 TCGA-A5-A2K7 
        7.92        36.33         9.60         8.02         5.33         5.16 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
        1.97        19.79         2.40         3.02         1.12         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
        1.68        14.66        22.49         1.28         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW 
       20.65        15.62         1.94        15.95         1.87         2.33 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
       83.67        23.31        86.07         8.22        39.42        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89         7.86        12.20        20.91       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        16.24         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       34.98        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        28.54        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       19.20        16.96        13.55        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 
       54.12        67.50        25.12        36.39        71.24        33.53 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       27.32        31.13        38.70         0.10         0.33         0.13 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
       20.52         0.13         1.18         8.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        11.01         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       191.84        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD 
       11.70        11.87        15.29        62.14        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98         7.92        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       12.56        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        24.13        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        23.93         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O 
       36.36        37.51        36.79        27.42        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         0.69         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        0.26         4.27        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       35.38         9.37        12.39        31.10        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
        7.99        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KW TCGA-EY-A1G7 
       24.79        19.36        35.15        12.89        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR 
       23.90        22.78        13.97         6.90        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 
       19.33        18.87        22.82        31.04        13.84         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        6.97         3.72         5.29        40.01        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        7.99        13.84         8.98         9.07        28.93        28.96 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       41.06         1.74         2.43        10.82         4.21         5.52 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.03               0.10 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            125.42             191.84 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            17.850             24.215 
[1] "0.0 - 125.4 (17.9)" "0.1 - 191.8 (24.2)"
[1] "hr=" "2.2"
D67V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  15Q LOSS MUTATED                                        33
  15Q LOSS WILD-TYPE                                     334
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  15Q LOSS MUTATED                               8
  15Q LOSS WILD-TYPE                            12
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  15Q LOSS MUTATED                                  53
  15Q LOSS WILD-TYPE                                45
D67V3, multiclass
                                         clus
vv                                        15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               33                334
  MIXED SEROUS AND ENDOMETRIOID                          8                 12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     53                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V4, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    19  75
  15Q LOSS WILD-TYPE 119 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     19   75
  15Q LOSS WILD-TYPE  119  272
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                19                119
  YES               75                272
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    60   4   6   7
  15Q LOSS WILD-TYPE 276  18  11  22
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               60                276
  R1                4                 18
  R2                6                 11
  RX                7                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     2
  15Q LOSS WILD-TYPE                                4    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  15Q LOSS MUTATED                          20
  15Q LOSS WILD-TYPE                        53
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  15Q LOSS MUTATED                                           2    62
  15Q LOSS WILD-TYPE                                         7   293
D67V6, multiclass
                                           clus
vv                                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                               20                 53
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   62                293
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2  65
  15Q LOSS WILD-TYPE  11 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   65
  15Q LOSS WILD-TYPE   11  271
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               65                271
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    68  15
  16P LOSS WILD-TYPE 355  45
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                83                400 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                15                 45 
$`16P LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LO 
       65.75        60.53        11.44        36.33        28.64         7.33 
TCGA-AJ-A23M TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3NH 
        1.18         0.85         0.49        22.26         1.35         0.76 
TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LF 
        1.71        21.99        45.53        36.89        48.79         3.39 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A1C9 
       97.71        41.95        18.25        53.92        28.54        15.25 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2IO 
       12.43        76.83        11.08        30.12        71.24        38.70 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JT 
        0.13         0.20         0.03         0.13         0.13        43.13 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY 
       17.85         4.11        75.72        36.82       102.31        11.87 
TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0MU TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC 
        5.03        34.95        20.28        15.45         6.81        10.22 
TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16G TCGA-D1-A16J 
       10.16        16.64        49.55        22.55        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NW 
       31.07         6.77        28.08        11.15        13.22         0.72 
TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
        2.07         4.27         4.11        35.38         9.37        91.96 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 
       10.92        10.78        32.38        19.40        27.16        26.96 
TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
        6.90        17.62        12.59        29.10        27.35        13.84 
TCGA-EY-A4KR TCGA-FI-A2EU TCGA-FI-A3PV TCGA-KJ-A3U4 TCGA-PG-A5BC 
        6.44        96.69        41.06         2.43        10.82 

$`16P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       42.35        15.95         7.92         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O 
       46.32         5.33         5.16        14.96         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.39        19.79         2.40         3.02         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
        2.24         1.68         1.64        14.66        22.49         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
        0.92        36.99        20.65        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 
        1.87        16.87         2.33        83.67         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05N TCGA-AP-A05O 
       86.07         8.22        39.42        57.80         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        33.73         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA 
       65.88        13.28        19.20        16.96        13.55        20.28 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
        4.77        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        27.32         2.96        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.23         0.10         0.33        20.52         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
        8.35        14.47        80.38        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        23.01        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 
       50.89        14.40        14.70        11.70        15.29        12.79 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VT 
       43.04        39.32        30.81        21.17        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
       11.31        35.90        34.98         6.21        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        67.20        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
        8.55         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16O 
       37.32        36.36        37.51        36.79        11.51        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         1.41         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       19.53         6.64        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.01        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.51         1.78        24.30         2.33        22.92         1.41 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DI-A0WH 
        3.52        41.42         8.48        44.88         0.26        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       39.29        36.62        24.30        12.39        31.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80         7.99        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.28        24.79        34.39        19.36        35.15        12.89 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       22.26        16.34         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT 
       13.97        19.27        18.84        17.88        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 
       12.43        15.81         8.55         6.48        19.33         3.62 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        13.45        45.76        31.04 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       34.98        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        26.01 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74        13.15         4.21         5.52 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.03               0.10 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            102.31             191.84 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            17.620             23.425 
[1] "0.0 - 102.3 (17.6)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2"  
D68V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16P LOSS MUTATED                                        29
  16P LOSS WILD-TYPE                                     338
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16P LOSS MUTATED                               6
  16P LOSS WILD-TYPE                            14
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16P LOSS MUTATED                                  49
  16P LOSS WILD-TYPE                                49
D68V3, multiclass
                                         clus
vv                                        16P LOSS MUTATED 16P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               29                338
  MIXED SEROUS AND ENDOMETRIOID                          6                 14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     49                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V4, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    19  65
  16P LOSS WILD-TYPE 119 282
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     19   65
  16P LOSS WILD-TYPE  119  282
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                19                119
  YES               65                282
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    47   5   7   8
  16P LOSS WILD-TYPE 289  17  10  21
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               47                289
  R1                5                 17
  R2                7                 10
  RX                8                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     2
  16P LOSS WILD-TYPE                                4    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16P LOSS MUTATED                          20
  16P LOSS WILD-TYPE                        53
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16P LOSS MUTATED                                           2    54
  16P LOSS WILD-TYPE                                         7   301
D68V6, multiclass
                                           clus
vv                                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                               20                 53
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   54                301
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     3  55
  16P LOSS WILD-TYPE  10 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3   55
  16P LOSS WILD-TYPE   10  281
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               55                281
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   101  20
  16Q LOSS WILD-TYPE 322  40
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               121                362 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                20                 40 
$`16Q LOSS MUTATED`
TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH 
       87.32        65.75        60.53        17.59        11.44        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QM 
       91.04        28.64         7.33         1.18         1.08         0.85 
TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A052 
        0.49        22.26         1.35         0.76         1.71        21.99 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LF TCGA-AP-A0LI 
       57.80        45.53        36.89        48.79         3.39        97.71 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A05U TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW 
       41.95        18.25        29.69        53.92        28.54        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CI 
       16.96        15.25        20.28        12.43        76.83        72.56 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HD 
       25.12        36.39        11.08        30.12        71.24        40.50 
TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       19.36         2.96        38.70         0.33         0.13         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K6 
       20.52         0.03         0.13         0.13        43.13        13.74 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS 
       17.85         4.11       113.36        75.72        36.82       102.31 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0MU 
       11.87        12.79         5.03        34.95        36.49        20.28 
TCGA-BG-A0VT TCGA-BG-A0VW TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A2AE 
       24.39        16.34        12.56        13.78        15.45        23.70 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ 
        6.81        10.22        16.64        61.87        49.55        22.55 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A17R 
       27.42        29.92        31.07         6.77        28.08        11.15 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH 
       13.22         0.72        18.25         2.07         4.27         4.11 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 
       35.38         9.37        31.10        91.96        48.36        10.92 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 
       10.78        32.38        19.40        34.39        27.16        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A214 
       22.26        16.34         6.90        17.62        12.59        14.40 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2CY 
       29.10        27.35        13.84         6.44        17.92        34.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-KJ-A3U4 
       96.69        59.01         9.07        28.93        41.06         2.43 
TCGA-PG-A5BC 
       10.82 

$`16Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP 
        3.22       105.37        74.10        57.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.96        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        7.92         9.60         8.02        46.32         5.33         5.16 
TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.96         1.97         0.39        19.79         2.40         3.02 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76         2.24         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.49         1.28         0.92        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AP-A051 
        1.94        15.95         1.87        16.87         2.33        83.67 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N 
        5.95        23.31        86.07         8.22        39.42         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.20        20.91       125.42       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO 
       30.90        10.42        27.85        16.24        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        19.82        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        35.01        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A1CK 
       13.28        19.20        13.55        20.05        54.12        67.50 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HG 
        4.77        33.53        61.18        68.71        33.40        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G7 
       17.75        27.32        31.13         0.23         0.10         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18         8.35        14.47        80.38        56.91        46.75 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K9 
       30.51        25.91        23.01        17.88        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
        8.71       185.79        88.34        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       191.84        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A5OC 
       14.40        14.70        11.70        15.29        62.14        41.06 
TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.13        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98         7.92        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       21.17        15.42        26.66        34.29        28.54        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       56.58        14.83        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        1.81         9.57        35.67        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       34.98         6.21        10.16        31.76        24.99        24.13 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       37.51        36.79        11.51        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ 
       24.30         2.33        22.92         1.41        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       44.88         0.26        16.31        39.29        36.62        24.30 
TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       12.39        23.38        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80         7.99        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       27.12        32.28        24.79        19.36        35.15        12.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO 
       23.34        23.34        23.90        22.78        13.97        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.88        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM 
        8.55         6.48        19.33         3.62        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.45        45.76        31.04         2.14         6.97         3.72 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.29        40.01        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ 
        8.98        28.96        25.02        26.01         1.74        13.15 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.03               0.10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            113.36             191.84 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             20.28              23.36 
[1] "0.0 - 113.4 (20.3)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1.7"
D69V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  16Q LOSS MUTATED                                        49
  16Q LOSS WILD-TYPE                                     318
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  16Q LOSS MUTATED                               7
  16Q LOSS WILD-TYPE                            13
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  16Q LOSS MUTATED                                  66
  16Q LOSS WILD-TYPE                                32
D69V3, multiclass
                                         clus
vv                                        16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               49                318
  MIXED SEROUS AND ENDOMETRIOID                          7                 13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     66                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V4, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    27  95
  16Q LOSS WILD-TYPE 111 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     27   95
  16Q LOSS WILD-TYPE  111  252
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                27                111
  YES               95                252
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    72   8   8  10
  16Q LOSS WILD-TYPE 264  14   9  19
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               72                264
  R1                8                 14
  R2                8                  9
  RX               10                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  1     2
  16Q LOSS WILD-TYPE                                3    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  16Q LOSS MUTATED                          29
  16Q LOSS WILD-TYPE                        44
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  16Q LOSS MUTATED                                           2    79
  16Q LOSS WILD-TYPE                                         7   276
D69V6, multiclass
                                           clus
vv                                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                               29                 44
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   79                276
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3  82
  16Q LOSS WILD-TYPE  10 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   82
  16Q LOSS WILD-TYPE   10  254
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               82                254
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    87  21
  17P LOSS WILD-TYPE 336  39
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               108                375 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                21                 39 
$`17P LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH 
       65.75        60.53        36.82        19.96        11.44        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK 
       91.04        28.64         7.33         1.18         1.08         0.39 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NF 
        0.49         1.12         2.24        22.26         1.28         1.35 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D 
        0.76        16.87         1.71         5.95        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A1DQ 
       45.53        48.79       125.42        36.36        97.71        41.95 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A1C7 TCGA-AX-A1C8 
       33.73         0.56        53.92        28.54        16.96        13.55 
TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HF 
       76.83        11.08         4.77        71.24        61.18        19.36 
TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
       17.75        38.70         0.33         0.13         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I 
        0.03         0.13         0.23        17.85         4.11        75.72 
TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A0M6 
       43.96       102.31        11.87        12.79         5.03         7.92 
TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0U9 
       36.49        15.45         6.81        10.16        24.13        67.20 
TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16I 
       49.55        29.95        22.55        39.48        37.32        11.51 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3DH 
       31.07        18.67        13.22         0.72        18.25         4.11 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-EO-A1Y5 
       35.38         9.37        12.39        31.10        48.36        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
        7.99        10.78        19.40        22.26        16.34         4.54 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A210 
       23.90         6.90        17.62        15.09         8.55        12.59 
TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-FI-A2CY 
        3.62        29.10         6.44        17.92         3.72        34.98 
TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-KJ-A3U4 TCGA-PG-A5BC 
       36.00        28.93        25.02        41.06         2.43        10.82 

$`17P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        7.92         9.60         8.02        46.32         5.33         5.16 
TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.96         1.97        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3IA 
        0.76         1.68         1.64        14.66        22.49         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62         1.94        15.95         1.87 
TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        2.33        83.67        21.99        23.31        86.07         8.22 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89         7.86        12.20        20.91       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
        3.39        63.16        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA 
       40.11        65.88        13.28        19.20        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       12.43        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       36.39        30.12        33.53        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        27.32         2.96        31.13         0.23         0.10 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18         8.35        14.47         0.13        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        11.01         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       88.34        54.44        45.90        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       191.84        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       11.70        15.29        62.14        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.22        31.76        24.99        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       19.79         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O 
       36.36        37.51        36.79        27.42        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       22.92         1.41        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        0.26         4.27        16.31        39.29        36.62        24.30 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       91.96        23.38        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.36        16.80        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       32.28        24.79        32.38        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       12.89        27.16        26.96         6.21        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        17.88        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
        6.48        19.33        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 
       45.76        31.04        27.35        13.84         2.14         6.97 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
        5.29        40.01        33.99         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR 
       96.69        59.01         9.07        28.96        26.01         1.74 
TCGA-K6-A3WQ TCGA-QS-A5YQ TCGA-QS-A5YR 
       13.15         4.21         5.52 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.03               0.10 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            125.42             191.84 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            17.685             24.300 
[1] "0.0 - 125.4 (17.7)" "0.1 - 191.8 (24.3)"
[1] "hr=" "2.3"
D70V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17P LOSS MUTATED                                        39
  17P LOSS WILD-TYPE                                     328
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17P LOSS MUTATED                               9
  17P LOSS WILD-TYPE                            11
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17P LOSS MUTATED                                  61
  17P LOSS WILD-TYPE                                37
D70V3, multiclass
                                         clus
vv                                        17P LOSS MUTATED 17P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               39                328
  MIXED SEROUS AND ENDOMETRIOID                          9                 11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     61                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V4, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    28  81
  17P LOSS WILD-TYPE 110 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     28   81
  17P LOSS WILD-TYPE  110  266
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                28                110
  YES               81                266
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED    69   8   6   9
  17P LOSS WILD-TYPE 267  14  11  20
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               69                267
  R1                8                 14
  R2                6                 11
  RX                9                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  1     1
  17P LOSS WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17P LOSS MUTATED                          25
  17P LOSS WILD-TYPE                        48
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17P LOSS MUTATED                                           3    72
  17P LOSS WILD-TYPE                                         6   283
D70V6, multiclass
                                           clus
vv                                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                               25                 48
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                3                  6
  WHITE                                                   72                283
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4  75
  17P LOSS WILD-TYPE   9 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4   75
  17P LOSS WILD-TYPE    9  261
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  9
  NOT HISPANIC OR LATINO               75                261
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    64  14
  17Q LOSS WILD-TYPE 359  46
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                78                405 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                14                 46 
$`17Q LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       65.75        60.53        19.96        11.44        36.33        91.04 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD 
        7.33         1.18         1.08         0.39         0.85         0.49 
TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3TW 
        2.24        22.26         1.28         1.35         0.76         1.71 
TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
        5.95        39.42        57.80        45.53        48.79       125.42 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A1CR TCGA-AX-A2H5 
       97.71        41.95        33.73         0.56        11.08        71.24 
TCGA-AX-A2H8 TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
       61.18        17.75        38.70         0.13         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A3S1 TCGA-BG-A0M8 
        0.13         0.23        43.96       102.31         5.03        36.49 
TCGA-BG-A18C TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ 
       15.45        10.16        24.13        67.20        49.55        22.55 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW 
       37.32        11.51        31.07         6.77        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A3DH TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LZ 
       18.25         4.11         9.37        12.39        31.10        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
       10.92         7.99        10.78        22.26        16.34         4.54 
TCGA-EY-A1GJ TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2OQ 
       23.90        17.62         8.55        12.59         3.62        29.10 
TCGA-EY-A547 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-KJ-A3U4 
       17.92        34.98        36.00        28.93        25.02         2.43 

$`17Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 
       15.95         7.92         9.60         8.02        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN 
        5.33         5.16        14.96         1.97        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        3.02         1.12         0.76         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.49         0.92        36.99        20.65        15.62         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
       15.95         1.87        16.87         2.33        83.67        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       23.31        86.07         8.22        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T 
       10.42        27.85        16.24        18.25        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 
       54.12        67.50        25.12        36.39         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       33.53        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       27.32         2.96        31.13         0.23         0.10         0.33 
TCGA-AX-A3G3 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.03         1.18         8.35        14.47         0.13        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       17.88        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       45.90        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      191.84        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       15.29        12.79        62.14        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       28.54        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       35.67        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       34.98         6.21        10.22        31.76        24.99        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        23.47        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.79        27.42        29.92        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QY 
       16.31        39.29        36.62        24.30        35.38        91.96 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       16.80        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       24.79        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       12.89        27.16        26.96         6.21        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT 
        6.90        19.27        18.84        17.88        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 
       12.43        15.81         6.48        19.33        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        13.45        45.76        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
        6.44         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       33.99         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ 
        9.07        28.96        26.01        41.06         1.74        13.15 
TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       10.82         4.21         5.52 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.13               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            125.42             191.84 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            17.685             23.470 
[1] "0.1 - 125.4 (17.7)" "0.0 - 191.8 (23.5)"
[1] "hr=" "1.9"
D71V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  17Q LOSS MUTATED                                        32
  17Q LOSS WILD-TYPE                                     335
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  17Q LOSS MUTATED                               7
  17Q LOSS WILD-TYPE                            13
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  17Q LOSS MUTATED                                  40
  17Q LOSS WILD-TYPE                                58
D71V3, multiclass
                                         clus
vv                                        17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               32                335
  MIXED SEROUS AND ENDOMETRIOID                          7                 13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     40                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V4, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    19  60
  17Q LOSS WILD-TYPE 119 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     19   60
  17Q LOSS WILD-TYPE  119  287
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                19                119
  YES               60                287
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    53   6   3   7
  17Q LOSS WILD-TYPE 283  16  14  22
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               53                283
  R1                6                 16
  R2                3                 14
  RX                7                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  1     1
  17Q LOSS WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  17Q LOSS MUTATED                          11
  17Q LOSS WILD-TYPE                        62
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  17Q LOSS MUTATED                                           3    57
  17Q LOSS WILD-TYPE                                         6   298
D71V6, multiclass
                                           clus
vv                                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                               11                 62
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                3                  6
  WHITE                                                   57                298
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     5  53
  17Q LOSS WILD-TYPE   8 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5   53
  17Q LOSS WILD-TYPE    8  283
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  8
  NOT HISPANIC OR LATINO               53                283
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    37   7
  18P LOSS WILD-TYPE 386  53
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                44                439 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 53 
$`18P LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO 
       65.75        60.53        17.59        46.32        28.64         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QM TCGA-AJ-A3BF TCGA-AP-A05H TCGA-AP-A0LH 
       14.96         1.18         0.85         1.12        45.53        36.36 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
       11.08         4.77        71.24         0.20        20.52         0.03 
TCGA-B5-A11P TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI 
       36.82        15.45         6.81        10.16        16.64        61.87 
TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A1NW 
       49.55        22.55        11.51        18.67        28.08         0.72 
TCGA-D1-A1O0 TCGA-DI-A2QU TCGA-EO-A2CG TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO 
        2.07        31.10        32.38        16.34         4.54        19.27 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A3QX 
       18.84        15.09         8.55        14.40        45.76        13.84 
TCGA-FI-A2EW TCGA-FI-A2EX 
       59.01         9.07 

$`18P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        19.96        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       91.04         5.33         5.16         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI 
       19.79         2.40         3.02         0.49         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        0.92        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       39.42        57.80        36.89         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       33.73         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       25.12        36.39        30.12        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.13         0.13         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.13        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC 
       14.70        11.70        11.87        15.29        12.79        62.14 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
        5.03        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       10.22        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02         6.77         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
        4.11        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
        9.37        12.39        91.96        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.99        10.78        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       32.28        24.79        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        26.96        22.26         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT 
       22.78        13.97         6.90        17.88        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       12.43        15.81         6.48        19.33        12.59         3.62 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       18.87        22.82        13.45        31.04        29.10        27.35 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
        6.44        17.92         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        34.98        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
        8.98        96.69        28.93        28.96        25.02        26.01 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ 
       41.06         1.74        13.15         2.43        10.82         4.21 
TCGA-QS-A5YR 
        5.52 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.03               0.10 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             71.24             191.84 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             16.49              23.38 
[1] "0.0 - 71.2 (16.5)"  "0.1 - 191.8 (23.4)"
[1] "hr=" "1.6"
D72V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18P LOSS MUTATED                                        20
  18P LOSS WILD-TYPE                                     347
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18P LOSS MUTATED                               5
  18P LOSS WILD-TYPE                            15
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18P LOSS MUTATED                                  19
  18P LOSS WILD-TYPE                                79
D72V3, multiclass
                                         clus
vv                                        18P LOSS MUTATED 18P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               20                347
  MIXED SEROUS AND ENDOMETRIOID                          5                 15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     19                 79
[1] 3 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, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     9  35
  18P LOSS WILD-TYPE 129 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      9   35
  18P LOSS WILD-TYPE  129  312
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 9                129
  YES               35                312
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    30   5   1   2
  18P LOSS WILD-TYPE 306  17  16  27
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               30                306
  R1                5                 17
  R2                1                 16
  RX                2                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     1
  18P LOSS WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18P LOSS MUTATED                           6
  18P LOSS WILD-TYPE                        67
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18P LOSS MUTATED                                           1    35
  18P LOSS WILD-TYPE                                         8   320
D72V6, multiclass
                                           clus
vv                                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                6                 67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   35                320
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1  35
  18P LOSS WILD-TYPE  12 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1   35
  18P LOSS WILD-TYPE   12  301
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               35                301
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    47   8
  18Q LOSS WILD-TYPE 376  52
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                55                428 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 52 
$`18Q LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K3 
       65.75        60.53        36.82        17.59        11.44        46.32 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF 
       28.64         7.33        14.96         1.18         0.49         1.12 
TCGA-AP-A05H TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 
       45.53        36.36        97.71        20.28        11.08         4.77 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A11P 
        0.20        20.52         0.03         0.13         0.13        36.82 
TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD 
       34.95        15.45         6.81        10.22        10.16        16.64 
TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K 
       49.55        22.55        37.32        18.67         1.41        28.08 
TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
        0.72         2.07         4.11        31.10        91.96        48.36 
TCGA-EO-A2CG TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW 
       32.38         4.54        19.27        18.84        15.09         8.55 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A3QX TCGA-FI-A2CY TCGA-FI-A2EW 
       14.40        13.45        45.76        13.84        34.98        59.01 
TCGA-FI-A2EX 
        9.07 

$`18Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.96        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 
        7.92        36.33         9.60         8.02        91.04         5.33 
TCGA-A5-A2K7 TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        5.16         1.08         1.97         0.39        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        2.40         3.02         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26         1.28         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65         1.35        15.62         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
        1.87        16.87         1.71         2.33        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        39.42        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89         7.86        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37         3.39        63.16        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        16.24        18.25        33.73         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.55        15.25        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 
       54.12        67.50        25.12        36.39        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.23         0.10         0.33         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        8.35        14.47        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14         5.03        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        24.13        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41        13.22        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DI-A0WH 
       41.42         8.48        44.88         0.26         4.27        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92         7.99        10.78        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       33.01        27.12        32.28        24.79        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.36        35.15        12.89        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       16.34         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.88        17.62        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP 
       19.33        12.59         3.62        18.87        22.82        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       29.10        27.35         6.44        17.92         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        3.72         5.29        40.01        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       13.84         8.98        96.69        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC 
       26.01        41.06         1.74        13.15         2.43        10.82 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.03               0.10 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             97.71             191.84 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            16.640             23.425 
[1] "0.0 - 97.7 (16.6)"  "0.1 - 191.8 (23.4)"
[1] "hr=" "1.5"
D73V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  18Q LOSS MUTATED                                        23
  18Q LOSS WILD-TYPE                                     344
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  18Q LOSS MUTATED                               6
  18Q LOSS WILD-TYPE                            14
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  18Q LOSS MUTATED                                  26
  18Q LOSS WILD-TYPE                                72
D73V3, multiclass
                                         clus
vv                                        18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               23                344
  MIXED SEROUS AND ENDOMETRIOID                          6                 14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     26                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V4, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    12  43
  18Q LOSS WILD-TYPE 126 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     12   43
  18Q LOSS WILD-TYPE  126  304
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                12                126
  YES               43                304
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED    35   5   3   4
  18Q LOSS WILD-TYPE 301  17  14  25
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               35                301
  R1                5                 17
  R2                3                 14
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     2
  18Q LOSS WILD-TYPE                                4    17
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  18Q LOSS MUTATED                          14
  18Q LOSS WILD-TYPE                        59
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  18Q LOSS MUTATED                                           2    37
  18Q LOSS WILD-TYPE                                         7   318
D73V6, multiclass
                                           clus
vv                                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    2                 17
  BLACK OR AFRICAN AMERICAN                               14                 59
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   37                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"
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     2  44
  18Q LOSS WILD-TYPE  11 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   44
  18Q LOSS WILD-TYPE   11  292
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 11
  NOT HISPANIC OR LATINO               44                292
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    38  14
  19P LOSS WILD-TYPE 385  46
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                52                431 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                 46 
$`19P LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO 
       65.75        60.53        11.44        46.32        28.64         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EJ 
       14.96         1.18         1.08         0.49         1.12         1.64 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A3K1 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H5 
       39.42        45.53        18.25        20.28        76.83        71.24 
TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0KB 
        2.96         0.20         0.03         0.23         0.13         4.11 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MU TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV 
       75.72        36.82        50.89         7.92        36.49        12.56 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16I 
       15.45         6.81        67.20        39.48        27.42        11.51 
TCGA-D1-A16N TCGA-DI-A2QT TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EY-A1GP TCGA-EY-A1GV 
       31.07        12.39        10.78        19.40        18.84        15.81 
TCGA-EY-A1GW TCGA-EY-A214 TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2CY TCGA-FI-A2D2 
        8.55        14.40        27.35        13.84        34.98        36.00 
TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-KJ-A3U4 
       96.69         9.07        28.93         2.43 

$`19P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       42.35        15.95         7.92        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       91.04         5.33         5.16         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        0.85         2.40         3.02         0.76         2.24         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26         1.28         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65         1.35        15.62         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
        1.87        16.87         1.71         2.33        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J 
        5.95        23.31        86.07         8.22        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        33.73         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       13.55        15.25        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        27.32        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 
        0.10         0.33         0.13        20.52         0.13         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        8.35        14.47        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84       102.31        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       11.87        15.29        12.79        62.14         5.03        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        34.98        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        28.54        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        23.47 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        88.34        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J TCGA-D1-A16O 
       37.32        36.36        37.51        36.79        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         1.41         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02         6.77         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
        4.11        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
        9.37        31.10        91.96        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
        7.99        31.96        35.05        33.01        27.12        32.28 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        32.38        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       27.16        26.96        22.26        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ 
       23.90        22.78        13.97         6.90        19.27        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 
       17.62        15.09        16.11        12.43         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       12.59         3.62        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       31.04        29.10         6.44        17.92         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        3.72         5.29        40.01        33.99         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
        8.98        59.01        28.96        25.02        26.01        41.06 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
        1.74        13.15        10.82         4.21         5.52 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.03               0.10 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             96.69             191.84 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             15.63              23.34 
[1] "0.0 - 96.7 (15.6)"  "0.1 - 191.8 (23.3)"
[1] "hr=" "3"  
D74V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19P LOSS MUTATED                                        16
  19P LOSS WILD-TYPE                                     351
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19P LOSS MUTATED                               4
  19P LOSS WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19P LOSS MUTATED                                  33
  19P LOSS WILD-TYPE                                65
D74V3, multiclass
                                         clus
vv                                        19P LOSS MUTATED 19P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               16                351
  MIXED SEROUS AND ENDOMETRIOID                          4                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     33                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V4, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    14  39
  19P LOSS WILD-TYPE 124 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     14   39
  19P LOSS WILD-TYPE  124  308
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                14                124
  YES               39                308
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    31   4   4   4
  19P LOSS WILD-TYPE 305  18  13  25
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               31                305
  R1                4                 18
  R2                4                 13
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  1     1
  19P LOSS WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19P LOSS MUTATED                           8
  19P LOSS WILD-TYPE                        65
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19P LOSS MUTATED                                           1    39
  19P LOSS WILD-TYPE                                         8   316
D74V6, multiclass
                                           clus
vv                                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                8                 65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   39                316
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3  36
  19P LOSS WILD-TYPE  10 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3   36
  19P LOSS WILD-TYPE   10  300
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               36                300
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    35  14
  19Q LOSS WILD-TYPE 388  46
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                49                434 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                14                 46 
$`19Q LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       65.75        60.53        28.64         7.33         1.18         1.08 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3NF 
        0.85         0.49         1.12         2.24         1.64         1.35 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A3K1 TCGA-AX-A2H5 
       39.42        45.53       125.42        36.36        18.25        71.24 
TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A11I 
        2.96         0.20         0.03         0.23         0.13        75.72 
TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C 
       36.82       102.31        50.89        36.49        12.56        15.45 
TCGA-BG-A3PP TCGA-BS-A0U9 TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16N TCGA-DI-A2QT 
        6.81        67.20        27.42        11.51        31.07        12.39 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A214 
        7.99        10.78        19.40        23.90         8.55        14.40 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EX 
       27.35        13.84        34.98        36.00        96.69         9.07 
TCGA-KJ-A3U4 
        2.43 

$`19Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       42.35        15.95         7.92        11.44        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
        8.02        91.04        46.32         5.33         5.16        14.96 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        1.97         0.39        19.79         2.40         3.02         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.68        14.66        22.49        22.26         1.28         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        15.62         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 
        1.87        16.87         1.71         2.33        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J 
        5.95        23.31        86.07         8.22        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        12.20        20.91        48.79       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        33.73         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        27.32        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 
        0.10         0.33         0.13        20.52         0.13         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        8.35        14.47        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        54.44        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       17.36        16.57       191.84        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       11.87        15.29        12.79        62.14         5.03        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98         7.92        38.37        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        28.54        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        35.67        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       29.92        33.63        10.65         0.69        18.67         1.41 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27         4.11        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       24.30        35.38         9.37        31.10        91.96        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        10.92        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       32.28        24.79        32.38        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       12.89        27.16        26.96        22.26        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33        12.59         3.62        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 
       13.45        45.76        31.04        29.10         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 
        2.14         6.97         3.72         5.29        40.01        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F4 
        7.99        13.84         8.98        59.01        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC 
       25.02        26.01        41.06         1.74        13.15        10.82 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.03               0.10 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            125.42             191.84 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             14.40              23.26 
[1] "0.0 - 125.4 (14.4)" "0.1 - 191.8 (23.3)"
[1] "hr=" "3.1"
D75V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  19Q LOSS MUTATED                                        16
  19Q LOSS WILD-TYPE                                     351
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  19Q LOSS MUTATED                               4
  19Q LOSS WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  19Q LOSS MUTATED                                  30
  19Q LOSS WILD-TYPE                                68
D75V3, multiclass
                                         clus
vv                                        19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               16                351
  MIXED SEROUS AND ENDOMETRIOID                          4                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     30                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V4, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    11  39
  19Q LOSS WILD-TYPE 127 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     11   39
  19Q LOSS WILD-TYPE  127  308
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                11                127
  YES               39                308
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    29   3   3   5
  19Q LOSS WILD-TYPE 307  19  14  24
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               29                307
  R1                3                 19
  R2                3                 14
  RX                5                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  1     0
  19Q LOSS WILD-TYPE                                3    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  19Q LOSS MUTATED                           6
  19Q LOSS WILD-TYPE                        67
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  19Q LOSS MUTATED                                           1    38
  19Q LOSS WILD-TYPE                                         8   317
D75V6, multiclass
                                           clus
vv                                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                                6                 67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   38                317
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     3  32
  19Q LOSS WILD-TYPE  10 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3   32
  19Q LOSS WILD-TYPE   10  304
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 10
  NOT HISPANIC OR LATINO               32                304
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    13   3
  20P LOSS WILD-TYPE 410  57
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                16                467 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 57 
$`20P LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A3BD TCGA-AP-A05H TCGA-AP-A0LI 
      149.56        60.53        19.96         0.49        45.53        97.71 
TCGA-AW-A1PO TCGA-AX-A1CF TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-B5-A0K8 TCGA-BG-A0M6 
        0.56        76.83        20.52         0.13        17.85         7.92 
TCGA-BG-A0MO TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-FI-A2D2 
       43.04        23.90         8.55        36.00 

$`20P LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        0.85         2.40         3.02         1.12         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        0.92        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       39.42        57.80        36.89         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       33.73        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.33         0.13         0.20         0.03         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       12.79        62.14         5.03        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       35.67        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        67.20        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         1.41         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02         6.77         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
        4.11        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10        91.96        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       27.12        32.28        24.79        32.38        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.36        35.15        12.89        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       19.27        18.84        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       12.43        15.81         6.48        19.33        12.59         3.62 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        13.45        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       29.10        27.35        13.84         6.44        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        6.97         3.72         5.29        40.01        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
       28.93        28.96        25.02        26.01        41.06         1.74 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       13.15         2.43        10.82         4.21         5.52 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.13               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            149.56             191.84 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             22.21              22.82 
[1] "0.1 - 149.6 (22.2)" "0.0 - 191.8 (22.8)"
[1] "hr=" "1.3"
D76V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20P LOSS MUTATED                                         7
  20P LOSS WILD-TYPE                                     360
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20P LOSS MUTATED                               1
  20P LOSS WILD-TYPE                            19
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20P LOSS MUTATED                                   8
  20P LOSS WILD-TYPE                                90
D76V3, multiclass
                                         clus
vv                                        20P LOSS MUTATED 20P LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                7                360
  MIXED SEROUS AND ENDOMETRIOID                          1                 19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      8                 90
[1] 3 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, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     8   8
  20P LOSS WILD-TYPE 130 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8    8
  20P LOSS WILD-TYPE  130  339
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 8                130
  YES                8                339
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    10   1   2   0
  20P LOSS WILD-TYPE 326  21  15  29
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               10                326
  R1                1                 21
  R2                2                 15
  RX                0                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     1
  20P LOSS WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20P LOSS MUTATED                           2
  20P LOSS WILD-TYPE                        71
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20P LOSS MUTATED                                           1    11
  20P LOSS WILD-TYPE                                         8   344
D76V6, multiclass
                                           clus
vv                                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                2                 71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   11                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"
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  11
  20P LOSS WILD-TYPE  12 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   11
  20P LOSS WILD-TYPE   12  325
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               11                325
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     8   0
  20Q LOSS WILD-TYPE 415  60
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                475 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 0                 60 
$`20Q LOSS MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A3BD TCGA-AW-A1PO TCGA-D1-A0ZZ 
      149.56        60.53        19.96         0.49         0.56        22.55 
TCGA-EY-A1GJ TCGA-FI-A2D2 
       23.90        36.00 

$`20Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        0.85         2.40         3.02         1.12         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        0.92        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       39.42        57.80        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        18.25        33.73        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        27.32         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       38.70         0.23         0.10         0.33         0.13         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.03         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       14.47         0.13        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       12.79        62.14         5.03        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        28.54        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        35.90        34.98         6.21        10.22        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.76        24.99        24.13        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        23.47        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27         4.11        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       35.38         9.37        12.39        31.10        91.96        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92         7.99        10.78        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       33.01        27.12        32.28        24.79        32.38        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
       34.39        19.36        35.15        12.89        27.16        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       22.26        16.34         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
        6.90        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59         3.62        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       34.98        33.99         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       59.01         9.07        28.93        28.96        25.02        26.01 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-QS-A5YQ 
       41.06         1.74        13.15         2.43        10.82         4.21 
TCGA-QS-A5YR 
        5.52 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.49               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            149.56             191.84 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            23.225             22.820 
[1] "0.5 - 149.6 (23.2)" "0.0 - 191.8 (22.8)"
[1] "hr="     "9400000"
D77V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  20Q LOSS MUTATED                                         3
  20Q LOSS WILD-TYPE                                     364
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  20Q LOSS MUTATED                               2
  20Q LOSS WILD-TYPE                            18
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  20Q LOSS MUTATED                                   3
  20Q LOSS WILD-TYPE                                95
D77V3, multiclass
                                         clus
vv                                        20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                3                364
  MIXED SEROUS AND ENDOMETRIOID                          2                 18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                      3                 95
[1] 3 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, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   3
  20Q LOSS WILD-TYPE 133 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    3
  20Q LOSS WILD-TYPE  133  344
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 5                133
  YES                3                344
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     8   0   0   0
  20Q LOSS WILD-TYPE 328  22  17  29
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                8                328
  R1                0                 22
  R2                0                 17
  RX                0                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     1
  20Q LOSS WILD-TYPE                                4    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  20Q LOSS MUTATED                           1
  20Q LOSS WILD-TYPE                        72
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  20Q LOSS MUTATED                                           0     5
  20Q LOSS WILD-TYPE                                         9   350
D77V6, multiclass
                                           clus
vv                                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                                1                 72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                0                  9
  WHITE                                                    5                350
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   7
  20Q LOSS WILD-TYPE  13 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    7
  20Q LOSS WILD-TYPE   13  329
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 13
  NOT HISPANIC OR LATINO                7                329
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    37  10
  21Q LOSS WILD-TYPE 386  50
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                47                436 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                10                 50 
$`21Q LOSS MUTATED`
TCGA-A5-A0GN TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A3BG 
       60.53        36.33        46.32         1.18         1.97         0.76 
TCGA-AP-A052 TCGA-AP-A05D TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A3K1 
       21.99        57.80       125.42         3.39        97.71        18.25 
TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A2HF TCGA-AX-A2IO TCGA-AX-A3G4 
       53.92        37.78        20.28        19.36        38.70         0.13 
TCGA-B5-A1N2 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 
       12.79         7.92        36.49        15.45         6.81        10.16 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A179 TCGA-D1-A3DG TCGA-DI-A1NN TCGA-DI-A1NO 
       22.55        39.48         6.77         4.27        35.38         9.37 
TCGA-E6-A1LX TCGA-EO-A2CH TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GL TCGA-EY-A1GO 
       23.38        19.40        16.34         4.54        13.97        19.27 
TCGA-EY-A1GP TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A4KR TCGA-EY-A54A 
       18.84         3.62        14.40        45.76         6.44         3.72 
TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-PG-A5BC 
       36.00        28.93        25.02         1.74        10.82 

$`21Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95         7.92        11.44         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        8.02        91.04        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.96         1.08         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        3.02         0.49         1.12         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26         1.28         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65         1.35        15.62         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A053 
        1.87        16.87         1.71         2.33        83.67         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07         8.22        39.42        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        12.20        20.91        48.79       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       33.73         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        13.55        15.25        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       33.40        40.50        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13         0.23         0.10         0.33         0.13         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       20.52         0.03         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.13        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FC 
       14.40        14.70        11.70        11.87        15.29        62.14 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
        5.03        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        34.98        38.37        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        28.54        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B 
       11.31        35.90        34.98         6.21        10.22        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93         1.74         4.44        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         1.41         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1BU 
        8.48        44.88         0.26         4.11        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
       36.62        24.30        12.39        31.10        91.96        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92         7.99        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU 
       27.12        32.28        24.79        32.38        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 
       35.15        12.89        27.16        26.96        22.26         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       23.90        22.78         6.90        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ 
       12.59        18.87        22.82        13.45        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       27.35        13.84        17.92         2.14         6.97         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        34.98        33.99         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV 
       96.69        59.01         9.07        28.96        26.01        41.06 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-QS-A5YQ TCGA-QS-A5YR 
       13.15         2.43         4.21         5.52 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.13               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            125.42             191.84 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            18.840             23.405 
[1] "0.1 - 125.4 (18.8)" "0.0 - 191.8 (23.4)"
[1] "hr=" "2.2"
D78V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  21Q LOSS MUTATED                                        17
  21Q LOSS WILD-TYPE                                     350
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  21Q LOSS MUTATED                               4
  21Q LOSS WILD-TYPE                            16
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  21Q LOSS MUTATED                                  27
  21Q LOSS WILD-TYPE                                71
D78V3, multiclass
                                         clus
vv                                        21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               17                350
  MIXED SEROUS AND ENDOMETRIOID                          4                 16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     27                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V4, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    14  34
  21Q LOSS WILD-TYPE 124 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     14   34
  21Q LOSS WILD-TYPE  124  313
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                14                124
  YES               34                313
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED    33   2   4   4
  21Q LOSS WILD-TYPE 303  20  13  25
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               33                303
  R1                2                 20
  R2                4                 13
  RX                4                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     0
  21Q LOSS WILD-TYPE                                4    19
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  21Q LOSS MUTATED                          10
  21Q LOSS WILD-TYPE                        63
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  21Q LOSS MUTATED                                           1    35
  21Q LOSS WILD-TYPE                                         8   320
D78V6, multiclass
                                           clus
vv                                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         0                  4
  ASIAN                                                    0                 19
  BLACK OR AFRICAN AMERICAN                               10                 63
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                1                  8
  WHITE                                                   35                320
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  35
  21Q LOSS WILD-TYPE  12 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   35
  21Q LOSS WILD-TYPE   12  301
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 12
  NOT HISPANIC OR LATINO               35                301
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    77  16
  22Q LOSS WILD-TYPE 346  44
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                93                390 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                16                 44 
$`22Q LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OH TCGA-A5-A2K2 
       65.75        60.53        36.82        17.59        36.33        91.04 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A3BD 
        7.33        14.96         1.08         0.39        19.79         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NH 
        1.12         2.24         1.64         1.28         0.92         0.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A1DQ 
       16.87         1.71        57.80        45.53        48.79        41.95 
TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA 
       33.73        53.92        37.78        16.96        13.55        20.28 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HF 
       36.39        11.08        30.12        71.24        61.18        19.36 
TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        2.96         0.33         0.13        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU 
        0.23         4.11        75.72        36.82       102.31        50.89 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BG-A0VZ TCGA-BG-A0YV 
       11.87        12.79        34.13        36.49        28.54        12.56 
TCGA-BG-A18C TCGA-BG-A2AD TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-D1-A0ZP 
       15.45        35.67         6.81        10.22        67.20        29.95 
TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K 
       22.55        11.51        31.07        18.67         1.41        28.08 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A3DG TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU 
       13.22         0.72         4.27        35.38        12.39        31.10 
TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ 
        7.99        32.38        27.16        16.34         4.54        23.90 
TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A214 
        6.90        18.84        17.62         8.55        12.59        14.40 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A547 TCGA-FI-A2D2 TCGA-FI-A2F9 
       13.45        45.76        29.10        17.92        36.00        26.01 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
        1.74        13.15         2.43 

$`22Q LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.96        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 
        7.92        11.44         9.60         8.02        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A2QN 
        5.33         5.16         1.18         1.97         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        3.02         0.76         1.68        14.66        22.49        22.26 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65         1.35        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        1.87         2.33        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07         8.22        39.42        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D 
       46.45        35.34        45.99        66.58        34.98        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        65.88        13.28        19.20        15.25 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       25.12         4.77        33.53        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        27.32        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.10         0.20         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       191.84 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A3S1 
       14.40        14.70        11.70        15.29        62.14         5.03 
TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98         7.92        38.37        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       16.34        34.29        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       10.16        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        19.79         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.79        27.42        29.92        33.63        10.65         0.69 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY 
       24.30         2.33        22.92         1.41        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DI-A0WH 
       41.42         8.48        44.88         0.26         4.11        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LX 
       39.29        36.62        24.30         9.37        91.96        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        10.78        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       27.12        32.28        24.79        19.40        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 
       35.15        12.89        26.96        22.26         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK 
        8.15        24.36        27.16        23.34        23.34        22.78 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97        19.27        17.88        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM 
       15.81         6.48        19.33         3.62        18.87        22.82 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 
       31.04        27.35        13.84         6.44         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        3.72         5.29        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-PG-A5BC TCGA-QS-A5YQ TCGA-QS-A5YR 
       28.96        25.02        41.06        10.82         4.21         5.52 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.03               0.10 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            102.31             191.84 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            17.590             23.585 
[1] "0.0 - 102.3 (17.6)" "0.1 - 191.8 (23.6)"
[1] "hr=" "1.9"
D79V2, continuous
                    vv
clus                 ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  22Q LOSS MUTATED                                        39
  22Q LOSS WILD-TYPE                                     328
                    vv
clus                 MIXED SEROUS AND ENDOMETRIOID
  22Q LOSS MUTATED                              10
  22Q LOSS WILD-TYPE                            10
                    vv
clus                 SEROUS ENDOMETRIAL ADENOCARCINOMA
  22Q LOSS MUTATED                                  45
  22Q LOSS WILD-TYPE                                53
D79V3, multiclass
                                         clus
vv                                        22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA               39                328
  MIXED SEROUS AND ENDOMETRIOID                         10                 10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                     45                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V4, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    19  75
  22Q LOSS WILD-TYPE 119 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     19   75
  22Q LOSS WILD-TYPE  119  272
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                19                119
  YES               75                272
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    60   6   4   7
  22Q LOSS WILD-TYPE 276  16  13  22
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               60                276
  R1                6                 16
  R2                4                 13
  RX                7                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     1
  22Q LOSS WILD-TYPE                                3    18
                    vv
clus                 BLACK OR AFRICAN AMERICAN
  22Q LOSS MUTATED                          20
  22Q LOSS WILD-TYPE                        53
                    vv
clus                 NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  22Q LOSS MUTATED                                           2    67
  22Q LOSS WILD-TYPE                                         7   288
D79V6, multiclass
                                           clus
vv                                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                         1                  3
  ASIAN                                                    1                 18
  BLACK OR AFRICAN AMERICAN                               20                 53
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                2                  7
  WHITE                                                   67                288
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     5  68
  22Q LOSS WILD-TYPE   8 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5   68
  22Q LOSS WILD-TYPE    8  268
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                  8
  NOT HISPANIC OR LATINO               68                268
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    51  13
  XQ LOSS WILD-TYPE 372  47
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               64               419 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               13                47 
$`XQ LOSS MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-AJ-A2QM TCGA-AJ-A3BF 
       65.75        60.53        19.96        91.04         0.85         1.12 
TCGA-AJ-A3I9 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A0LF 
        1.28        21.99         5.95        57.80        36.89         3.39 
TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A1CK 
       41.95         0.56        53.92        16.96        76.83        67.50 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-B5-A0JN 
       11.08         4.77        19.36         0.03         0.13        80.38 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A5OE 
       23.01        17.85        36.82       102.31        12.79        34.95 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BK-A139 TCGA-D1-A0ZZ TCGA-D1-A16N 
       36.49        12.56        15.45        10.16        22.55        31.07 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 
       18.67         1.41         6.77        28.08        13.22         2.07 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A3AS 
        4.27         4.11         9.37        12.39        91.96        34.39 
TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW 
       16.34        23.90        18.84        17.62        15.09         8.55 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       29.10        13.84         6.44        36.00        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A3PV TCGA-KJ-A3U4 TCGA-PG-A5BC 
       28.93        41.06         2.43        10.82 

$`XQ LOSS WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        1.18         1.08         1.97         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        3.02         0.49         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26         0.92        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
        1.35        15.62         0.76         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
       16.87         1.71         2.33        83.67        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        39.42        45.53         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       25.12        36.39        30.12        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       68.71        33.40        40.50        26.33        17.75        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.13         0.20        20.52         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.13        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB 
       25.91        17.88        13.74        17.10        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       45.90        43.96        40.50        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      191.84        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       15.29        62.14         5.03        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        28.54 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       10.22        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        67.20        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        23.93         1.74         4.44 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         0.69         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QU 
       16.31        39.29        36.62        24.30        35.38        31.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92         7.99        10.78        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       35.05        33.01        27.12        32.28        24.79        32.38 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
       19.40        19.36        35.15        12.89        27.16        26.96 
TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       22.26         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       19.27        17.88        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       19.33        12.59         3.62        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A547 TCGA-EY-A548 
       13.45        45.76        31.04        27.35        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        6.97         3.72         5.29        40.01        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F8 
        7.99        13.84         8.98        96.69        28.96        25.02 
TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-QS-A5YQ TCGA-QS-A5YR 
       26.01         1.74        13.15         4.21         5.52 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.03              0.10 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           102.31            191.84 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           17.735            23.470 
[1] "0.0 - 102.3 (17.7)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.1"
D80V2, continuous
                   vv
clus                ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  XQ LOSS MUTATED                                        27
  XQ LOSS WILD-TYPE                                     340
                   vv
clus                MIXED SEROUS AND ENDOMETRIOID
  XQ LOSS MUTATED                               3
  XQ LOSS WILD-TYPE                            17
                   vv
clus                SEROUS ENDOMETRIAL ADENOCARCINOMA
  XQ LOSS MUTATED                                  34
  XQ LOSS WILD-TYPE                                64
D80V3, multiclass
                                         clus
vv                                        XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA              27               340
  MIXED SEROUS AND ENDOMETRIOID                         3                17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                    34                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V4, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    12  52
  XQ LOSS WILD-TYPE 126 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     12   52
  XQ LOSS WILD-TYPE  126  295
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               12               126
  YES              52               295
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    41   2   5   5
  XQ LOSS WILD-TYPE 295  20  12  24
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              41               295
  R1               2                20
  R2               5                12
  RX               5                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  1     0
  XQ LOSS WILD-TYPE                                3    19
                   vv
clus                BLACK OR AFRICAN AMERICAN
  XQ LOSS MUTATED                          15
  XQ LOSS WILD-TYPE                        58
                   vv
clus                NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  XQ LOSS MUTATED                                           1    44
  XQ LOSS WILD-TYPE                                         8   311
D80V6, multiclass
                                           clus
vv                                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                        1                 3
  ASIAN                                                   0                19
  BLACK OR AFRICAN AMERICAN                              15                58
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER               1                 8
  WHITE                                                  44               311
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     4  45
  XQ LOSS WILD-TYPE   9 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4   45
  XQ LOSS WILD-TYPE    9  291
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 9
  NOT HISPANIC OR LATINO              45               291
[1] 2 2
[1] FALSE
